Parts like the fenderliners would probably be OEMR only, with very little aftermarket. You could try TeamCherokee.com (they do a lot of soft parts like that,) or ask a buddy at a body shop where they get theirs (you do have a buddy in a body shop, don't you?)
For the THM700R4 - why for? The AW4 is often compared favourably to the 700, and I've been inside both boxes - the AW4 is simpler and more robust. Also, the early THM700R4 should be avoided at all costs - they were just plain trash up until 1990 or so (they have a fatal flaw which I don't quite recall - but it can't be fixed even with a full overhaul. Easier to just replace it with a later model.) The 4L60 is the same box, the 4L60E is an electronically-controlled version.
However, knowing what I know, I'd stick with the AW4 if that's what you have already (I think the gear ratios are also better.) The THM700R4 can be built up to about the same durability as you get with the AW4 from the factory - it came OEM behind the turbocharged six in the Celica Supra, and lived a good long while in that application...