Well, if you're going that built, and keeping the automatic AND having it built up, then sure, get that 3" exhaust... But I wouldn't suggest it until you actually get the turbocharger, and/or swap in a KL-03/KL-ZE or something... Even the 2.5L KL-ZE wouldn't gain much of anything, IF anything from a 3" exhaust as opposed to a 2.5". The angle mounted option would remove the rear muffler on the Racing Beat exhaust, which is what keeps it as quiet as it is. If you're going to do that, just grab an eBay cat back, and slap it on that.
A smaller turbo, such as the T25 or GT28R/RS will spool quickly, but boost will be limited to however much is efficient... Sure, you could go with more, but at that point, you're overworking the turbocharger. For that matter, even with a built auto (I'm not sure if this has been done yet), it's uncertain how much power you'll be able to hold. I know the 4E-AT on the SVX, after a performance rebuild, would be limited to about 400chp, at most. That's only up from a stock of 330chp. Pretty much ANY MTX can hold more than that on the SVX. STi, 2.5RS, and so-forth.
The intake manifold option for you would either to go with the '00 Federal Emissions manifold, which works pretty well. The stock manifold would work fine, and can be ported and polished, and modified heavily to work better than stock (I've done about 20+ of these now... Uugh.)
Your plans, as far as power goes, look to be aiming for nowhere above the 200whp mark. Hopefully, the ATX should be able to handle that if built up, but again, this is uncertain. I would say, as far as where to start, you should just save your cash for the transmission rebuild, block, and turbo kit... That's probably going to be upward of 10k in total, right there.