turkmenistan: no troubles, just rules
first of all: the pamir highway: no prob whatsoever, even the afghan border loop. there's actually 3 roads: murghab-khorog (all tarmac, really easy, 1 day), murghab via ishkashim to khorog (mostly gravel and some sand, but not all that hard, 2/3 days) and a loop murghab-roshkala-khorog (much more difficult, rocky and rivercrossings which might be high-3 days + check if roshkala is on your GBAo stamp explicitly). the 'worst' part of the pamir so-called highway is dushanbe-khorog: not difficult but all washboard, potholes and rubble. give or take 2/3 days. checkpoints are no hassle. if you have other questions, just ask.
turkmenistan depends on your budget. very easy country and no trouble, just procedure. the visa:
transit: you get 5/7 days but pass through in 3 or you'll have trouble on the outgoing border if you don't have hotel registrations. don't miss darvaza and keep in mind you'll have to ride the shortest route between your entry and exit point - they note it on your insurance and check at every checkpoint
if you can afford it, a tourist visa plus guide and driver (via stantours or other) will give you unlimited time & travel opportunities. the country is genuinly beautiful. don't miss darvaza. and if you get the change, check out the south-west (only hearsay/pictures but it looks great). the merv-turkmenabat passage is ugly desert. ashgabat-konya-urgench is much nicer.
borders are ok, just spent 4 hours there. and smile. but it is really really hot in summer.