Stock transmission won't work- D series transmissions won't bolt onto a B series engine.
The LS transmission has really long gears and a taller final drive. It'll work in a pinch, but it sucks.
The GSR transmission is set up more for performance- tighter gearing, better spaced gear ratios, and a shorter final drive. It's not nearly as short as a B16 or ITR transmission, but it's a good bit better for acceleration compared to the LS transmission. This should be your choice (along with a good LSD) for a turbo setup.