Yes, you can't run a 6 speed with a stock WRX drive shaft. The 6 speed is too long. The driveshaft from a WRX and auto is a little shorter to accommodate the longer tranny. I don't think an STI drive shaft will be long enough to run on a 5 speed but I've never tried. That rear diff you have should be a 3.54 which is the same as your 03 tranny. The 04 STI stuff should bolt right up and the axles should be okay. The STI driveshaft should bolt up just the same as your WRX one but I'm just afraid it'll be too short.