ok, yea something doesn't seem right with the rebuild if its only .10 over, headers and edelbrock intake and otherwise stock. Those things shouldn't have that big of an effect on drive-ability with a stock computer, at least not for 8k miles. The computer should have 'learned' to run right by now. I assume its not throwing any codes (Check Engine Light)?
compression / leak down check, yea. try a different dissy, yea if you have one to try.
To me it still seems like the computer is getting false feedback once it warms up and goes into open loop, but that would most likely cause a CEL. Maybe double check the main sensor connections and make sure there arent any frayed or stripped wires going to them... O2, TPS, MAP, etc.
Another thing to try is unplug or block off the EGR valve.
EDIT, is there any way to go back and verify with the rebuilder that everything was stock? Compression ratio, cam, head work, stroker, etc can have a huge effect on drive-ability with an untuned computer.