Final word... that sounds rather totalitarian...
Yes, I run the MAFT Pro in my car and I've installed and tuned a few for other people as well. If you have any issues with persistent error codes getting set in the ECU look at the link in my sig for some information about it; You'll also find a guide with details about many of the settings you'll find in the menu of the Gen II... there's more than you'll have as it's for the MAFT Pro, but the shared settings are relevant.
So, you're going to be running it like this:
Yeah, you'll need to tune. The cross sectional area is too different and there's not really enough room for the air flow to level out and flow evenly... you get a lot more air running over the hot wire then the surrounding area and as a result you run quite rich. The picture shows a 3.5" MAF and 2.75" intake pipe from my old N/A setup.
It's not a big deal and you're not going to run lean until you fix it... you'll run rich, but that's safe. Connect your wideband to the MAFT Gen II and learn how to tune.
I'd stick with the 3.5" since you have it and it's far less restrictive and you have a wideband with which to tune.