350 runs perfect with altenator disconnected.
 

1993 Chevrolet c2500 with 350 TBI.

Ran great, lifted the bed of the truck to fix pinched fuel filler line.

Set back down ran rough, smoked, no power-this prob a coincidence, but had to mention it.

After a lot of swapping and working, it will smooth out with low voltage.

Have you checked your ground connections between the block, firewall, and chassis? Check for continuity between each one. I have a similar truck. Perhaps you disturbed the fuel pump ground connection under the bed? If there's a bottleneck in the grounding system it may create strange symptoms when the alternator is attempting to put out a current and is unable to properly return ground voltage. I believe it is a 1-wire alternator like my 89' 2500. The 2-wire units use the second wire typically at a junction box to sense the voltage in the system to adjust its voltage accordingly. Start with checking continuity between grounds. You could also have the alternator tested.