Unplugging the MAF puts it into speed density and it uses the VE table that is in the computer.

I think you may indeed have a maf problem if when it was unplugged while running the fuel trims leveled out and was all normal but when plugged back in they went all whacky. If you have another car with a 3800, swap mafs.

If you are running a L36 throttle body, you will want that MAF table.

And make sure the injector data is correct if you swapped to GTP injectors, which I assume you must have.