Oops! Of course, you're absolutely right!
I have reworked the bogies to allow them to pass over switches and curves. In turn, I've had to raise the M motors by one plate, and then adjust the roof as well!
First, the bogies needed to be changed so they don't catch on points and curves. I felt the old structure wouldn't be strong enough as the lower plate is now missing.
The old 1x8 Technic beams were replaced by 4x4 Technic frames.
The two short 2-long axles were replaced by a single, longer axle. This forced the drive shaft to the motor to be shorter, and I've changed it to an axle with end stop. The end stop will help keep the bogie attached to the locomotive when I pick it up. The M motor is a weak link, but I think it will be easy enough to re-attach the bogies to the M motor if needed. Re-attaching the gear would be much harder.
In turn the M-motor mount has been pushed up:
And then, the motor was interfering with the roof so that had to change.
It worked out in the end though :).