Ok, I'm not sure I love this sh!t, but the older alternator is rated at 1100 watts and the newer ones are 1300 watts. Honda doesn't give us the actual amp rating, but it's probably 90A and 100A respectively. The rpm that it is spinning at isn't really important after it reaches the minimum for it to output a nominal load. That means the newer engine spinning it faster is not really what causes the higher output, it's the actual regulator and diode bridge that's used inside the unit. Your 03 will only get out what it needs so there's no danger in using the higher output unit in it. Now, with that said, you could feasibly add enough lighting and other electrical bobbles to load it to its full potential and that might cause an issue with the main fuse. The main fuse is sized for the system and bike and exceeding its size will blow it, but not because the alternator can handle it.
Rob's Candy Red '04