We changed the engine, new wires, plugs, new plenum, all new gaskets, o rings on fuel rack and a bunch more things. My question is, what may be left that would cause stumbling acceleration. It isn't the plugs because we ran existing plugs and it did it, changed to new and it still was the same. I unplugged each coil and noted a slowdown in the engine. I unplugged the electrical plug to each injector, noted a drop in idle with each. So i assume my plugs are fine, injectors are fine, and wires are fine. I changed the fuel filter, and it seems to have helped with acceleration (Once its going, it goes!) but it always seems to be a fight to get there. I'm assuming that it is more related to not the engine, but perhaps a sensor or something that did not come attached to the new motor. This problem has spanned 2 motors, and at first I thought it was merely a crappy 1st motor in the car, but when we changed it, and it an the same as before,i was fairly annoyed. It seems to be mostly with snappy acceleration and not so much with slow and steady.
As usual, any help would be appreciated.

first thought are tps, maf, map if any one of these acted it up it could and would cause it. ie if tps wasnt reading right it wouldnt know to send more fuel untill it read a lean code and that would slow it down a ton. maf sensor obvious flow issues. map if it read wrong it wouldnt know how much load and all that it was running correct me if im wrong those are my top 3 checks after what i read

1st priority: pull codes (good shop can do it for you if you do not have a scanner. If you want to have a scanner, AutoXray has one that works. I bought mine at Kragen Auto Supply). If there are codes, fix those things. If that does not solve the problem:

Some possibilities:
Weak fuel pump, obstructions in fuel lines. get a fuel pressure ga and test fuel pressure during acceleration.

Ignition control module: flat module underneath the three coils. Aftermarket OEM replacements are available at a fraction of the factory cost.

I second the previous poster'* nomination of a sensor, with the MAF sensor my first guess.

When was the last time you had the fuel injectors cleaned?

Do you hear any rattling from the catalytic converter?
One free test of back pressure is to pull the front O2.

Another thing would be to scan the car while running for the various engine parameters. That would tell you if the maf and sensors are working properly. Plus..if they were bad enough, you'd have codes from sensors.

There'* always the pcm. I like to think of 94 and 95 as the flakey years for pcm.

I don't have a scanner for the car sadly, it is one of those OBD1.5 messed up transition type things. The MAF seems fine. I unplugged it and the car almost stalled. I am under the impression that the MAF if not running right will make no difference to the car when unplugged. The injectors have never been cleaned, unless were talking about a gas additive.
All the coils are tested and doing well, but the rack that the coils mount to was never changed. It was clean when the new coils went on.
The car seems to run fine, no noise or rattles. When I 1st got the car, it ran well, but soon showed all the reasons the previous owner was selling it. It was pulled half apart 3 times before it died. After the last time inside it, it was running crappy, then threw a piston arm into my oil gallery. I assumed the motor was on its last legs and that'* why. Put this new motor in and it still happens.
I do not have anything to test fuel pressure handy, but i can get it. I have my doubts that it is the fuel, but its worth while to check.
Also, my car doesn't show engine light. Even when this happens there is nothing. And as an interesting side note, it is now raining today, and my car is running amazingly well. I took a drive today to buy some tickets, and I was noticing decent response. Tried to get it to do the baggy start, and it didn't. I don't know if that means anything outside of that my car likes rain?