Check the alternator output at the battery by reading battery voltage:-
engine off
Engine on PTO off
Engine on PTO on
Let us know the numbers to one decimal place
When you said you cleaned the engine, did you remove the blower housing and clean all of the cooling fins ?
If you have a compressor, stick an air duster under the flywheel and blow the dust out.
While you are there, pull the bolt out of the flywheel and check that the slot of the key is a perfect square.
Other than that, a weak throttle spring will allow the governor to hold the throttle plate a bit too far closed when the engine is under load
The service manual for your engine is available from Kohler ( sign in as a guest ) and some other places if you have problems getting it there.