There is usually a bearing or bushing in the end of the crankshaft that should be replaced. But I can’t locate that in the diagrams for your tractor! There is sometimes a dust seal there also.
The name of that is something like guide bushing in most cases, but Kubota will use a different name like dry bearing.
Also, note that the count of bolts seems to be too small. There are several bolt holes in the pressure plate. From another diagram you need two of #50 and #30 and 4 of #40.
There is also a clutch alignment tool that helps get the clutch plate centered in the pressure plate. You might want to check on that but most home mechanics just use a dowel rod that fits in the clutch and then the end of the crankcase. You are probably aware of the need for that.