If it was my tractor I would remove all items connected to engine...clutch, pto clutch and starter. Remove one at a time and try to spin the engine over. Maybe one of the above is causing your drag. I would remove the pto clutch first. If none ot the 3 is causing the drag on the engine you will have to take engine apart. When you remove the piston spin the crankshaft to see how free it is.
I had a Kohler K321 that made a noise after it ran a few minutes. The problem was the crankshaft bearing on the pto side. I've had a few that the bearing in the pto was bad and cause a noise and not leaving the pto clutch release.
Before you take the bearing plate off check to see how much crank end play is. A way to check crank end play is the way a Kohler manual shows.
You can download a Kohler manual from the site's Technical Library.
It is hard to tell what the problem is without having the tractor/engine in front of me.
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