1995 Mercury Marquis engine runs rough / stalls

I had a leak in the heater supply line ( it runs under the intake manifold) removed the manifold repaired the hose. at the same time I cleaned the egr channel in the throttle body ( it was clogged and the check engine light was on) Also the pcv line into the throttle body was leaking and I repaired that. after reassembling everything. the battery was disconnected throughtout the repair. I started the car, the check engine light was no longer on and it ran for about 2 minutes before shutting down. I found that the air filter was very dirty and tried running it without one with the same results. However when I ran the vehical with the air intake disconnected from the throttle body it stays running but after a few minutes it idles rough. At this point I suspected the MAF and tried running the car with everything assembled and the MAF disconnected, it ran but if I plug the sensor back in it stalls immediatly. So I figured it needs a new MAF sensor. After replacing the MAF sensor it still does the same thing.
I'm leaning toward the TPS (cleaning or replacing) But I want to avoid hit or miss part replacment.