BEAMS and Emissions..., Will a swap work with OBD2? Options

[Driver]

I was just curious if I were to swap a 3S red top into my '97 would it still work with the OBD2 emissions stuff? I don't know how Japan does their emissions control, and seeing as how I have to get my car tested every so often, I want to make sure it'll all hook up. I did a 20 valve swap into my '93 Corolla and everything, for the most part, plugged and played but it was old enough not to go in for testing and it didn't even have On Board Diagnostics, it just had Toyota's scan port.

Also, my car is auto, I've seen a few people had done manual conversions and Tweak from Phoenix Tuning has done quite a few, how hard is it really to do? If it's above my level of skill, I would be happy with leaving it auto and still swapping in a red top, I heard those came auto as well. Although... I have yet to see a single auto swap show up on the internet.