We need some pictures Millsi. Some of the things you have just said sound impossible or very unlikely. Please start by reading this thread:
https://www.outdoorking-forum.com.au/forum/u...amp;Main=6920&Number=34937#Post34937

The clutch countershaft has threads at the ends of the center square section the clutch hubs slide on. The nuts screwed onto these threads set the position of the clutches on the shaft, to keep them from sliding off sideways down the shaft rather than clamping.

Once you have the countershaft out of the mower, you can remove the sprocket, then the nuts, and slide the clutches and the two-way thrust bearing (with its springs and shims) off the shaft.

I'm having trouble imagining the clutches running out of true unless someone has intervened in an unlikely way with a very heavy implement. However when we see your pictures we may get further ahead with trying to help you.