Why is my Mercury Mariner skipping?

You mean the number two cylinder is still misfiring? Test compression ..... Test fuel injector. Good luck!

If I could share one recommendation to each person who works on their own cars, I'd tell them: you don't need to replace your "computer"!!! Almost never. 1984 in the age of non-writable processors? Maybe, and that's a big maybe. But today? Almost never. Replacing a "computer" without performing a "programmable module installation" procedure using a Ford IDS diagnostic tool on this Mercury is a disaster waiting to happen any way you look at it. And yes, a compression test would be helpful. Also, did you use original equipment Ford coils? That's a necessity.