LSD: limited slip differential.
G-series transmission: the transmission model mazda used w/ the BP engines.
"Add fuel w/ boost:" a turbocharger compresses the intake air, and thus the engine is taking in more air than normal. if you have more air, you need more fuel. your current ECU will not be able to compensate for the extra air a turbo will put into the cylinders.
it's probably not feasible to tweak the BPT ECU to work w/ an auto.
check out this FAQ:
http://web2.airmail.net/theman/protegefaq/
also, it sounds like you should do a lot more reading before you send corksport (or anyone) a lot of money. i'm not saying not to do the swap, but you'll be better off if you know what's going on. IMO, it'd be easier (and probably cheaper) to sell your auto car and buy a clean 5-speed LX. they're out there. that way you'll have the tranny you need, and you could even sell the engine to make back some of your $$$.