What Pat (harmonyards) said about the gearbox alignment is spot-on. By raising the front of the gearbox, you're actually forcing things into poor alignment. Your loco ran quieter that way, because the "balls" of the dogbone shaft coupling between the motor and the gearbox were constrained and no longer free to rattle around.
One thing to add: I think your existing motor is actually a Mabuchi RS-545. This is a small loco; I don't believe that Weaver used the RS-550 because it didn't fit, so unfortunately the 555 won't fit either. A small Pittman like a 9432 would be a nice upgrade over the stock motor, it would also reduce the top speed a little. But I don't think the motor is where most of the noise is coming from. There are other things you could do to mask the noise. But try to solve the root cause of the problem first!
