It sounds like the problem might be the second gear (idle gear I think they call it), snapping in and out against the case, which might be remedied by putting the pinion gear on backwards to keep it more or less against the case.
The other option is that the rear axle might be dirty or the wheels themselves may be scraping against the chassis every so often.
If a little clicking is the most of your problems I wouldn’t worry about it. Between the incessant gear mashing noise, the motor whine, and other issues, it sounds like you have few real problems, unlike my 9 cars…
-dan
