I owned a '03 G 6MT for several years. Great car.
Normally, I would caution against what you're planning. It's a HUGE undertaking.
However, if you have both cars, a lot of the hassles are removed. You'll need the entire wiring harness and gauge cluster from the donor car, as well as the driveshaft and axles. If you can keep the AT diff, I think it's a lower ratio (which would be cool).
We have the FSM for your reference here, and we'll be here for you throughout the swap... If you can do it all on the cheap, and replace worn/serviceable items as you go, go for it!