[Busted Tractor]

OOPs forgot to say the bolt heads can be cut off then the bolts act as long dowel pins. AND be sure there is room to take the bolts out when the engine is tight to the clutch housing.
Do NOT use bolts to pull the housings together, if you do you an damage something. The tractor should go together easily and almost completely (at least to the dowel pins) before pulling with bolts.

 

[I use red mn]

I would not recommend to “eyeball” your clutch alignment. It may work and slip together easy, but if it is off center by not much it will turn into a big wrestling match which may lead to damaging your clutch plate. You can get an alignment tool as shown in the link or you can set the pressure plate on the trans shaft then slide the clutch plate on the splines and slide the tractor together and bolt the pressure plate up through the starter hole. This is probably all “Greek” to you if you have never done a clutch job.
Dennis, how much extra horsepower you get out of that painted flywheel? ; > )
Clutch alignment tool

 

[Gopher Baroque]

@560Dennis Super A ?
You will need something to line up the clutch disk when the tractor is ready to go back together
There are tools for this, but you can also just "eyeball" it -- the disk has to be centered when looking at the splines and pilot bearing, and that is all that is needed
again use what is available to you

In one case, I have used a wood dowel with tape wrapping. Dowel to fit pilot bush in flywheel, tape to fit ID of clutch disk splines. Close enough to get it back together and do that first shift!