Yes, the new motors provide stronger vibration feeling but they start to run more abruptly which makes them harder to control at low values.
From one hand, you can make the vibration softer. First of all you can use Low - High dial at the remote control. By default it's disabled for USB mode, you can enable it via Gametrix Control Panel software.
If that's not enough, you can use reduced voltage power supply. For example. I use 9 Volts instead of 12 Volts with Robiton SN 1000 S universal power supply unit. It would make the motors behavior close to the motors used by Gametrix.
If that's still not enough we could arrange motor replacement with weaker motors.
From the other hand, I realize that you'd rather prefer to keep vibration strength high for most of the effects, but reduce the vibration level for a few selected effects like engine humming for example. I think a good approach to try would be reducing number of the motors engaged into those selected effects. For instance we could edit correspondent .uwv files so engine effect engaged just 2 motors located in the kidney area. I assume the overall vibration feeling would be essentially reduced for those effects. If that's fine with you we could make some adjustments and tests.