The mainshaft should have some endplay, about half the thickness of the circlip that retains the gear is typical. I'd guesstimate that at ~0.020". If there's substantially more, like the thickness of the circlip...or more than that, something's not quite right. I'd want to know where it originates. Most likely, it'd be the primary shaft walking inside the cases. Since the gear is mechanically coupled to the primary (input) shaft, via splines and there's a ball bearing on the other side, the gear hub is never going to wear. Were that not true, circlip failures would be as plentiful as opinions...except, of course, that there would be a thrust washer between it and the gear face. This is how the tranny is assembled; a thrust washer goes between each spinning gear and the circlip that retains it. The primay driven gear is considered a stationary gear, i.e. it doesn't spin on the shaft.
All of that having been said, I have my doubts about the primary driven gear being the source of your knocking. I've encountered knocking that resulted from mismatched primary drive gears. Stock primary gearing was either 17/69 or 18/67. The noisy setup I'm referring to was hybridized, unfortunately, I cannot recall if the cobbled-together motor had 18/69 or 17/67 fitted. You wouldn't think that a single tooth mismatch would be enough to cause problems, much less knocking...but it did. The key symptom here is that the noise only occurred while the bike was in motion. So, if you're getting this all the time the engine is running, it's probably not what you're dealing with.
OTOH, clutch noises aren't exceptionally rare. Worn pilot bushings even less so. Seems a good idea to check primary drive gear/pilot bushing fit, as well as anything that might be loose enough to rattle around inside the clutch...as well as verifying that the clutch is tight on the crankshaft.
