I'm sure you are running the correct gear mesh, but yes it's loud, and how did you adapt a 540 motor, as a 5mm shafts on the 550 is plenty stout to avoid any misalignment etc. from side loading under power. Are you running a 5mm pinion adapter, such as the ones from Robinson or Novak, those can lead to the pinion not being concentric if your running a 540 motor.

Post some pics.

Unless you plan on making the 48p gear 8+mm wide and a wide pinion, the gear will strip and more or less pick up a lot of debris. That's why 32p is so great, it holds a great tooth load and is almost self cleaning due to the root widths.

Plus once your tires bite, the greatest shock will be at the spur gear, or when you hit an obstacle with throttle still applied, so I'd suggest sticking with the 32p.

I have found that you can eliminate some of its play with 1/8 off road different shims and that will help keep it in line with the pinion and avoid deformation and possible damage.

If it's still too loud for you rather adapt to 08 mod such as those used in 1/8IC 4wd cars that may be a better route than 48p.