Never thought the 3.1/3.4 could even bolt onto our cars, so I bets it's neither of those.

Post picture of it.

Is the MAF inside the throttle body or somewhere else?

3.1 and 3.4 cars do NOT run a maf sensor in the throttle body, they run it in the intake tubing.

And yes running something different will effect how it runs, even more when not tuned for the changes.