OK... I'm about ready to lose it here.

I've been chasing a "ghost" for a month now and am running out of options to figure it out. Below I'll describe what I have, what I have done, etc. etc.
The vehicle:
1994 Plymouth Voyager SE 10th Anniversary Edition.
3.3 liter V6 with A604/41TE transmission
What has been done with the van.
2004 - March - Purchased for $50.00 with bad transmission (busted pin in diff) Van had 75,000 miles on it.
2004 - July - Put transmission from 1991 Dodge Grand Caravan in it.
- Also replaced plugs and wires.
Thru January 2006 - Drove as a daily vehicle. - normal/routing maint.
January 2006 - Transmission sharted to shift hard, go into limp mode, etc. etc. - Also noticed in late 2005 that check engine light would come on when I got outside of town... Problem code indicated EGR valve.
January 2006 - Memorial day weekend - Van was parked outside, next to garage.
Memorial Day weekend 2006 - Installed original transmission that had been rebuilt. - Used "drive and learn" technique to train transmission.
Started to notice occassional buck/kick at times. Couldn't determine if problem was electrical, engine, transmission, fuel, etc.
Last week. Problem getting worse, and now hearing an occassional POPing noise - Sounds like it is coming from drivers side, under hood. Possible firing in exhaust manifold/"Y" pipe?.
1) Put timing light on each spark plug wire. Sometimes light "misses" on #2 cylinder... Swapped plugs 2 & 4. Problem continues, swap plug wire on #2 from 1990 Dodge Carvan. Problem continues.
2) Replaced EGR valve - Problem continues
3) Swapped ignition pack today (put pack from 1991 Dodge Grand Caravan in). - Problem is much less, but new "symptoms"...
On cruise, van doesn't shift until 4000-5000 RPM... "Cruising speed" of 65/70 puts RPM at 3000... - Van is slow to leave from stops.
Parts I have available, that I can still swap out include:
Remaining 5 plug wires from 1990 Dodge Grand Caravan (a drivable spare)
All 6 plugs from 1990 Dodge Grand Caravan.
TSM from 1991 Dodge Grand Caravan... TSM has been unhooked from van and power since 1994.
I have at least 2 or 3 transmission solinoid packs that I can swap out as well. All are used but are from working transmissoin.
HELP!!!!
I'm not sure what to do at this point, but I'm going crazy here.
My wife asked if I'm ready to sell it and buy another vehicle... - I said "not sure yet." - That isn't a good response from me though because I hate to trade/sell good vehicles. - The van now has 87000 miles on it, and the body is in great shape.