Another problem could be the cam itself, the shop that did the grind may have screwed it up, seeing how the engine never performed properly from the start. If everything else checks out(i.e, vacuum, AFM, timing/t-chain, etc.), I would replace the cam w/stock one, and see if that helps, you should be able to pluck one from a P-n-P pretty cheap.

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed