Yes flywheel removed and faced.Tractor went together 2 turns on each bolt.not a slide right in.Had the tractor in neutral,started hard barely,engine lug then a shut down.I re split,ran the motor no lug no shutdown,so I figure in the clutch somewhere.Adjusted the 3 pto plate screws to.39" they were off,plare not moving in assembly,Also concerned about 3 plate/throw out bearing arms, real stiff ,so was the pedal.When you attach the assembly to the flywheel they compress a lot at 20lb torque.Got a hang up somewhere or maybe shouldent bought a $300 unit.
Your first statement is a HUGE OH NO.
You can NOT face a Kubota flywheel, especially when your dealing with a 2 stage clutch.
It changes the dimensions too much, and will make it when you can not disengage the clutch.
Now for the good news, that's not your issue.
Your issue is something is wrong with the clutch pack.
Either there is a setup or a manufacture error in the clutch or possibly an installation issue if the inside disk is installed backwards.
Hopefully where ever you got it has a good return policy.
When you get a 2 stage clutch pack you should not have to adjust anything, should be a direct bolt on.
Now this is a long shot, but on some models it's possible to put the throw-out bearing on backwards which will make the clutch hard to press and will mess with everything.
You should not have to have forced it together, it should slide right together.
Sometimes during assembly the clutch disks are not lined up and a quick pop of the clutch pedal will loosen it right up on assembly.