Rebuilt engine..cant get it to run right

I recently rebuilt my 302, went .040, had the shop assemble the short block, including a comp 268H. I had the tranny rebuilt (c-4), with a later valve body. Any ways the car is running.....but it smokes like a madman, The idle mixture screws do react when I turn them, but I cant get the smoke to die down. My PCV valve was broken and letting oil in soo I replaced it and ya still had smoke. Ive been doing the timing with a vacumm guage, getting a overall top reading of about 13 with out it fluctuating or stumbling too much. The car has a rough idle fluctuating in RPM and will sometimes stall on me. I was also getting rough shifts, (the tranny vacumm line is plugged into a intake vacumm port) soo I replaced my tranny vacumm line today and the shifts became less rough. The performance is there on the bottom end, if i accelerate from first to second it seems pretty stout, but once it hits second or third, blah nothing..... also when cruising at around 30-40 and i stomp on it, it will also have no pickup.....I was thinking maybe my vacumm advance. I have been doing the timing without it on. Another thing if i put it in drive and let off the brakes, the car will go then stop, go then stop, I think that has to do with the brakes grabbing alittle too much but i cant be too sure, the engine will fluctuate in RPM when doing this soo maybe it is engine related. Anyways, I need help and i really want this monster to run right! thanks guys

Mike

P.S. The plugs are gapped at .035" im running the petronix ignitor with a petronix ignitor coil, MSD 8mm wires. I have a few shorts in the car and I am waiting on a harness right now, but I dont think that would affect the performance. Also I have not adjusted the vacumm modulator at all, would that affect the pickup? Thanks again