Sorry I can't really help you with the missing road, we came in from Astrakhan - but it certainly looks from that jpg that a road does exist there.
I can tell you that there is indeed a very rough section of road between Aktobe and Aralsk. We rode it, it was tough, but dry so passable. The road itself is pretty bad but lorries and trucks have created tracks along either side of the 'road' so you can usually find a way to ride through.
To answer your Pamir Highway Q's:
My riding buddy didn't suffer from altittude sickness at all but I did. Not much, just shortness of breath and a mild headache. We looked into drugs beforehand but it was pretty low down on our list of priorities and we never got round to buying any. I suppose that if you are riding alone it is much more of an issue so I'd research AS on the web and follow the good advice available.
No rejetting was done. My BM has fuel injection and the other bike is an Africa Twin with carbs. By the time we got to the Pamir Highway we were both running on 80RON fuel anyway and neither bike suffered much from the altittude. Power was affected a little but we rode slow and steady over this section anyway and didn't find it a problem.
We camped along the highway for a few nights - mostly because it's a wonderful place to camp but also because finding accomodation en-route is difficult. There are homestays available - an organisation called MSDP runs a grass-roots network of places - we used one in Kala i Hussein which was a special experience for us, and there are others in Murghab, Khorog etc. Another night we pulled up in a tiny village and asked in a Kafe about sleeping, the owner put us up in a back room with food for very little money. When wild-camping the usual rules apply, get your bike off the road, but don't go wandering too far and beware of landmines particularly near the Afghan border and remember that it can get very cold at night - but basically we had no problems and loved it!
We did have stomach issues - ranging from the usual diorhea (SP?) often brought on by Russian
! to one episode each of proper food poisoning. The normal travellers' belly we just delt with and ignored but the food poisoning wasn't much fun. My colleague was laid up for 2 days with it in a horrible soviet hotel in Dushanbe - it was a shame that it was the same 2 days when a water pipe had burst and there was no running water in Dushanbe! We got a selection of anti-biotics from our doctors before we left and these really helped.
The actual Pamir Highway itself is in pretty good condition and is a wonderful ride - scenically spectacular, remote; everything you've read about basically. There are rough sections from about Sary Tash in Kyrgyz to Murghab and again from Khorog to Dushanbe (which offically isn't part of the PH) where some mountain sections were literally sliding down the mountain as we rode over them! But all in all it's a wonderful place to travel.
I'm happy to answer any other questions if you have them and if I can.