Have you replaced the clutch bell bearing recently? I can't get to the manual, my antivirus blocks it... lol!
Looking at the parts list, it appears to use a long needle type bearing:
https://rc.kyosho.com/en/nt025.html
https://rc.kyosho.com/en/97004.html
My old HPI NitroMT used one of those and they would get sloppy pretty quick allowing the clutch bell to float and not run as true. With a single speed, there's not as much deflection, but with a long bell for a 2-speed, wouldn't take much wear to allow it to move too much.
Looking at the chassis, the engine mount holes don't appear to be slotted, so I'd assume the gear mesh is fixed and cannot be adjusted. Hard to tell for certain since I can't look at the manual.