OK.. There re some likely things that can heppen to this 'unit' for 1, I have had to replace MANY sets of injectors in these for similar problems. Also, I do not see where you changed the fuel filter.. if it is clogged, this will happen also.
Another thing is that the TPS might not be putting out a 'steady' signal.. it could have a 'drop' in voltage from just being worn out on the inside.
Still another thing is that the EGR valve is not opening, or the ports are clogged.
Here is a picture of the diagnostic steps for when an engine stumbles on acceleration, because I know there are some things I forgot to mention:
So. what I would do to start.. is run the engine and pull each plug wire off (one at a time) while the engine is idling, and see if ALL cylinders change the way the engine idles when you pull the wire loose from the distributor cap. If they do, then all cylinders are working. If you remove one and the idle of the engine does not change.. then we will look into that cylinder a little closer.
If I have been helpful (so far) be sure to click Accept, so I can get credit for helping you.. and THEN, if you need more help with these test procedures or anything else, just let me know.. Fair?