Well the Supercharged cars are 2.93 ratio due to different sprockets on the drive chain. Swapping the Diff is easy but won't fix your different gear ratio, just makes it so you can use your axle and handle the extra load of the SC motor. As for using an 03 trans, I believe the 03 has an internal range selector switch, so you'll have to pull the side cover, remove that, install your external range selector from your old trans, and possibly switch out some solenoids from your old valvebody to the one in the 03 as well as the internal electrical harness. It would be a PITA to do but anything is possible.
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