Check for example http://geo.ebp.ch/gelaendeprofil/ for elevation information. But as this site is based on Google Maps, it doesn’t work in some places (like China) where Google is blocked.
I rated the road sections mostly based on the scenery, where ***** means that it is a must go and no star means „neutral“, i.e. that this part wasn’t spectacular at all for me. this rating depends of course also always on the weather I had during the time I cycled there.

some official information:

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Foreign nationals can only apply for Pakistan visa from their country of origin OR from the place of legal permanent residence. Request for visas of a THIRD COUNTRY origin will be decided only by the Ambassador/High Commissioner/Head of Mission/Consulate.

N
RPOs (Regional Passport Offices) have been authorized to extend tourist visa upto a maximum period of six months including the initial visa period and condone overstay upto 15 days on payment of visa fee subject to payment of a minimum of US $ 10 only.

unfortunately, i got arrested in quetta by the federal investigation agency (FIA) because i overstayed my visa (actually my first visa extension) for 12 days. i told the FIA that i was about to leave pakistan at taftan border, but they told me that i need a valid visa to leave pakistan. the FIA wanted to send me back to islamabad to get clearance from the ministry of interior. i showed them the official information mentioned above (N), but they didn’t know about that. i was also in contact with my embassy and told them about (N), but they got the information (i don’t know from whom), that RPO can only condone overstay upto 15 days on the original visa but not on an extension. but finally, i managed to convince the FIA after 48 hours to bring me to the RPO in quetta instead of sending me to islamabad and i got an extension (or actually a new visa) within one hour at RPO.

i know of other travellers who overstayed the visa, but all of them got an extension (mostly in lahore which seems to be very easy), so i don’t know what happens if you just show up at the border with an expired visa.

you can extend your visa in many places (probably in all RPO, although i didn’t find a list of the RPOs in pakistan), but the procedure is everywhere different, here some examples:
– lahore: same day.
– islamabad: 5 working days. maybe faster with the help of your embassy.
– gilgit: possible, but only if you have 2 days (or less) left on your valid visa.
– skardu: i did my extension in skardu. got 30 days extension for free after one hour. unfortunately, the extension starts already on the day of application!
– chitral: possible, but takes maybe up to 4 working days.
– quetta: got my second extension there within one hour, but people are arrogant and unfriendly.

the police was often worried about my safety in pakistan (although i consider most places i travelled as completely safe and definitely much safer than a lot of places in europe). usually, it is possible to camp (for free) at the PTDC motel. i recommend to do so, because otherwise it may happen that people are worried if they see you camping in the wild and they gonna call the police “for your safety” and then it’s just annoying. it’s also possible to ask directly at the police station to pitch the tent, usually they allowed. once it happened that the police showed me a place at a “goverment rest house”, but one hour later some “security guards” came and told me that i should continue for another 40km to sleep in a hotel. just refuse. the most annoying part for me was chitral – lowari pass – dir – swat.

Wagah – Lahore – Islamabad (September 2016)

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* Islamabad – Murree – Abbottabad – Mansehra (September 2016)

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**** Mansehra – Naran – Babusar Pass – Chilas (September 2016)

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unfortunately, i had a police escort all the way from mansehra to babusar top. but surprisingly i didn’t have an excort from babusar to chilas, although i always thought that this was the “dodgy party”. but it felt safe on both sides. i saw some old and “grumpy” men between babusar and chilas, but as soon as i said “as-salām(u) alaikum”, they usually smiled and responded with “wa-alaikum us-salām”, so i felt totally comfortable there. the police wanted me to stay in hotels, but i could convince them to sleep in my tent (in front of a guarded hotel or next to a police checkpoint).
the road over the pass is perfectly paved and the ride from babusar to chilas was one of the best i ever had: approximately 3000 meter of altitude difference!

** Chilas – Gilgit (KKH) (October 2016)

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****** Deosai Plains (Gilgit – Skardu – Deosai Plains – Astore – Gilgit) (October 2016)

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deosai was one of the most beautiful places i ever cycled! 8 dollar entrance fee for foreigners to deosai (40 cent for pakistani…). night temperatures (in october) were about -10C.
steep road from skardu to deosai (ali malik pass). i turned left on deosai (35.0758N, 75.5321E). bad road over a 4700m pass. another pass between saigar and faranshat. there was water at 34.6840N, 74.7372E. there is a shop in faranshat where you can get food. paved road after faranshat. checkpoint at faranshat. i could pass the checkpoint without problems. i stayed at the right hand side of shingo-river to gultari. unfortunately, some army-people stopped me after gultari and i got arrested, because this area is restricted area as it is so close to the line of control (LoC). even pakistani would need a permit to go there! the army brought me from gultari to chilum. more than 10 checkpoints on the way. one night and an interview later, i was released. but the arrest was not scary – i got free food and a lot of fruit juice. i had met a finnish motor biker in gilgit and he told me that he could ride all the way one week before, as the guys at the checkpoint just registered his bike. when i asked the officials in chilum, if i was the first foreign tourist who ended up so close to the line of control, they answered yes, thus nobody knew that the finnish biker was there a week before…
from chilum, i went east to the deosai plains again as i was not allowed to go anywhere south of chilum. there are some food tents at “bara pani” (35.0188N, 75.4148E). you can even see some bears nearby. i was lucky as i could join a pakistani family for free. i camped next to the food tents – and a bear was coming to our place after sunset and he was maybe only 50 meters away from us. so be careful! you aren’t allowed to take the road going south of bara pani. actually, the officer in gultari told me that you are not allowed to go anywhere south of the direct road from skardu to chilum, but there are no signs, thus you can always say that you didn’t know.

***** Hunza Valley (Gilgit – Khunjerab Pass – Gilgit) (October 2016)

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there are tunnels around attabad lake. the tunnels are absolutely dark!
khunjerab national park starts 35km north of sost. entry fee 8 dollar for foreigners (40 cent for pakistani). no problem to camp at the entrance checkpoint. but you are not allowed to camp inside the park (but i guess it’s no problem when you hide a bit). going all the way up to khunjerab and back in one day is hard if you have a fully loaded bicycle. i arrived at khunjerab pass in the evening, of course i was not allowed to sleep there, they said that i had to cycle back to the next checkpoint. there, i was not allowed to camp next to the checkpoint as you need special permission to pitch a tent – but i was allowed to sleep in a room of the checkpoint.
NOTE: you can’t cross the khunjerab pass. when you want to go from pakistan to china, you have to take a bus/taxi at sost.
from hunza valley, you can do a nice detour to shimshal, details below.

**** Shimshal Valley (October 2016)

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the road to shimshal starts some kilometer north of passu (i think the road starts at 36.4818N, 748839E and not at 36.5089N, 74.8716E).

*** Gilgit – Shandur Pass – Chitral (October 2016)

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i had police escort sometimes in gilgit-baltistan. i had an escort as well from mastuj to chitral (although i told them to leave, they stayed with me). in chitral, i could pitch my tent at the ptdc motel. but in the evening i had a police guard sitting in front of my tent – for my security. but this guard left in the night and slept at the police station, so it is totally ridiculous (but no worries, there is no reason for a guard!). actually, i was also not allowed to go alone to the bazar. the guard walked behind me with his gun.
get your “registration” in chitral at “foreigners registration office” (FRO), otherwise you might have problems when you want to travel further south. it took less than 2 hours to get the registration (for free).

* Kalasha (Bamburait) (November 2016)

you need the registration from chitral to visit kalasha valleys. there is a checkpoint at
35.7351N, 71.7749E where you need to show your registration from the FRO in chitral. there is another police checkpoint at 35.7381N, 71.7261E before the bridge, where you have to show your registration. just after the bridge, there is another checkpoint! there you have to pay 200rs “for the kalasha people”. a know a motorbiker who was escorted all the way and all the time in kalasha. as i left chitral without a guard (the guy who guarded my tent in chitral told me to wait – but i didn’t), i was able to cycle to bamburait without police. when the police at the checkpoints asked me “where is your security”, i just said “i don’t need security”. unfortunately, after some hours in bamburait i got a guard.

when you are coming from the south (peshawar) to kalasha, you probably have to go to chitral first to get the (ridiculous) registration, which is just another sheet of paper. you can try to cross the river at 35.6615N, 71.7584E: i took this bridge when i left the kalasha valley. there is an (army?) checkpoint there, but they didn’t ask for anything. but you probably have to show your registration later at the double-checkpoint (35.7381N, 71.7261E).

** Chitral – Lowari Pass – Dir – Timergara (November 2016)

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i was accompanied by the police all the time south of drosh. i was not allowed to sleep in my tent on the way to lowari pass, i had to sleep inside a police checkpoint, they locked my door from the outside for my securitiy(!). the road to lowari pass is rough and sometimes steep. registration/checkpoint on lowari pass. there is no longer a ptdc motel in/around dir. i was not allowed to camp as it is “too dangerous”. they wanted me to continue in the dark for nearly 80 km to the ptdc motel in timergara, but by the way, there is NO ptdc motel at timergara (although the police in dir assured me that there is a ptdc at timergara). in the end (after 3 hours of waiting and discussing with the police) i had to go to a hotel. before i told them that i want to camp, because otherwise (if it is too dangerous for camping) i would aks for 5 gunmen guarding my room. so in the end i had 5 armed police men guarding my room – hahaha…
i was not allowed to go from dir to kalam at 35.1634N, 718909E, they told me a bunch of bullshit-reasons like too cold, too much snow, road is blocked and terrorists. i got the information that you need a permit to go from swat to kalam to dir and that you can get this permit only in swat.
a few kilometers outside from timergara the police escort left and then i found out that there is no ptdc motel in timergara (for camping). without all the restrictions from the police, it would be much better for travelling and i would recommend to go there, but it was relatively annoying with all the restrictions and the waiting which was involved.

Timergara – Swat (November 2016)

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i was escorted all the way from timergara to swat. as far as i know you don’t need a NOC anymore to visit swat if you are travelling on a tourist visa. but the people at the checkpoint to swat didn’t know. i still had a my registration from chitral and then they took some copies of that. pakistani love paperwork and every paper will attract their attention. in swat, the police didn’t allow me to camp in front of a hotel as this is “very dangerous”. in the end i had to wait (very tired and extremely hungry) a very long time until they drove me to a hotel. i was not allowed to leave the hotel. they wanted to keep two guards inside(!) my room for my security. but i kicked them out of my room as they couldn’t be quiet when i tried to sleep. after all that bullshit and waiting i decided to go back to islamabad to be free again.
in my opinion, chitral, dir and swat are not dangerous and i’d love to travel there (especially also the road to kalam), but not when you have babysitters 24/7 telling you what to do. therefore i don’t recommend to go there.