I have an m5od-r2 that works very well, and I just wanted to know if it's normal to be a bit "chunkier" shifting into 2nd and 3rd gear. Maybe it's just user error, (my first manual)

No grinding
Good clutch/ no clutch problems
Rebuilt, no weird noises
I don't need to force anything at all, slides into all gears nicely

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Not sure what "chunkier" means, but if you mean it is stiff or you have to give a little more effort to shift.... it may be that the synchros are not lining up properly. My last m5od lasted 300k plus miles and shifted pretty good even when it wasn't fully disengaging the input shaft, and the "new" used one I put in shifts like butter.
Sounds like something is hanging, or maybe it is just the nature of the beast, it is a truck transmission.

 

It is a truck, f150, and it doesn't require any more effort, it just feels like a single small clack when I put it in, probably just how it's designed lol, like you said, the nature of the beast

 

Maybe change your trans fluid just for good luck...

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