If it makes you feel better I have the same kind of luck with my truck. I parked it in July when Colby came and got the old tranny and T-case from me. It sat for a few months until I had time to swap in the NV4500/203/205 and Alcan's.
I felt that I had been very thorough putting it all back together...yet it wouldn't start the first time I tried.

Replaced a couple of GP's, the GP relay and still had problems. I re-wired a plug in the circuit because wiggling it caused the GP's to work again...then eventually found the lug at the power distribution block on the firewall was loose.
How about this one...my first drive I find the steering seems spooky. My second drive I get Death Wobble, which i haven't had to deal with for three years. I check caster and find it has 10.5 degrees positive caster. So, I shim the front diff 4 degrees...steers better but I still have DW.

I add a washer to each king pin spring and drive it again and right away can tell the springs are bound. No death wobble, but steering is still scary with no return to center and a lot of wander. I order and install new bushings and king pin springs...seems OK. Temp drops to -12 C and we get 20" of snow and I start getting death wobble again...but too cold to do anything about it.
I end up adding a washer to the new springs and bushings...death wobble finally gone. Steering still seems a little weird though. I check the Toe-in and near as I can tell I now have 5/8" toe-in.
Getting the toe-in set up is today's project...if you care I'll update later. The weird part is that when I parked it it drove and steered great. 70 mph down the freeway with one finger on the wheel, no wander. I think the new king pin bushings changed my toe, because nothing has changed with the tie rod and the TRE's are still good.
The worst though is that when I rebuilt the NV4500 I overlooked adding a thin skim of RTV to the input shaft retainer housing...so my brandy new tranny weeps gear lube between the bell and tranny. I'll have to unbolt the works, slide it back and seal it up.
Rene