Summer Project Help....Please

Hello everyone I have an 01' gt auto and I'm doing an engine swap/stick conversion over the summer, but I want to finalize two more things, currently i have the stock 1zz-fe in my gt but im looking at going with a turbo 2zz-ge or a 4th gen 3s-gte i know stock the 3s can handle a larger psi of boost (my goal is 25psi) where as the 2zz is lighter but can handle about 8 psi max stock and with that does any one have any recommendations on what type of transmission to run as mine is currently auto and i want to swap it to stick because i don't think the 3s tranny will fit unless im mistaken.