Don't get discouraged yet, this is where the fun begins.
The first time I dropped a 540 into Micro it didn't work either. The idea was actually abandoned and only later, when I really sat down and thought about what had to be done, did it come together. And only after lots of trial and error - heavy on the trial and heavy on the error.
A 24T pinion is a good pinion to run for the brushed 480 motor, but in your case, with the hot esc and poor run time, I would start with the smallest pinion you can fit, which might be about a 16T to 18T. You may have to modify the rear bulkhead, sand it down a bit, but overgearing can be very hard on all the electronics.
Did you verify the pack is good? Replaced the dead cell? Smooth drivetrain? Gear mesh isn't too tight? You know, the typical things to look for. I'd start with the gearing, get it as low as possible. Upgrade the software in your esc. Try free-running the motor a few times, make sure it revs up nice and high. That's all I can think of at the moment. Keep us updated Adam, I know you'll get it cruising in no time.
Update: Actually after checking out the current draw specs on that motor, I'd say your cells are the limiting factor. Those kind of current numbers are consistant with stock 540-sized motors, and you can't run 540 motors on 2/3A cells, they just don't have the current capability, mainly due to high internal resistance (compared to standard Sub C cells). So all that current your brushless motor is trying to pull drops gobs of voltage in the cells thus dropping your voltage to the motor and, well, it ends up sucking. The only thing you can really do is run bigger cells (1/2SC or 4/5SC) or going Li-po. That might be a good experiment to see if you can get the motor to run better. Only thing, you can't easily fit 4/5SC cells in your sleeper, but you can fit a li-po. Just about any of the lipo packs in our recommended chart will fit. You jsut need a way to raise the pack over the belt.