What's your end goal for the car and for going turbo?
Do you want to go fast/make power?, do you want the challenge of doing something different? do you want street cred for the sweet sweet turbo noises?
IMO that's the main question, and that'll drive decisions on just about everything on a big project like this. Having a goal in mind helps with motivation when getting through the boring stuff too.
A boosted auto is breaking new ground (Or, it hasn't been done for a loooong time) so there's going to be lots of questions that'll only be answered by building the thing and seeing what breaks. Who knows the gearbox might be OK with your particular driving style, something else might be the weak link, or it might be a bulletproof combination that works really well
That's part of the fun and the challenge
4psi isn't going to do much apart from make noise, a teeny tiny intercooler would be enough (look at the small factory intercooler on the mazdaspeed cars running 6psi) if you even bother with one at all. An extra trans cooler probably isn't a bad idea. Emissions stuff will depend on your state/ local rules. I don't think there's any aftermarket parts for the auto box at all, even manual parts are hard to find.
Hopefully that's not too much of a downer. New and different projects are always interesting to see and a mildly built auto pro5 would be a sweet cruiser I reckon