Sounds like a blown fuse regarding the EATC. Maybe even you bumped a wire in your vacuum and EGR inspection.
Yes any engine from a Grand Marquis, Crown Victoria, Town Car, or 2 valve Mustang will fit. PCM will work fine. There may be a bit of coercing some parts. Is your intake manifold plastic? If so and the intake elbow (plenum) is pointed to the driver side and not the front of the car, you will be good to go. I forget the cut off year of the less friendly front-pointing intake manifold/plenum which makes things a tad more difficult. You will have to use your original fuel injectors and a few other parts if the engine doesn't come with it. There's a few gotcha's with the ECT sensors which may need a slight modification on newer model intake manifolds but nothing that's difficult.
And depending on the size of the vacuum leak, yes it may affect oil burning. Time will tell.