My Kohler Command 25 hp now runs WOT on its own

The governor gear has little tabs in the center of it that helps hold it in place when assembling the case. Kohler always recommended replacing the gear if it was ever removed from the little shaft that the governor gear rides on because the little tabs can be damaged when removing the gear from the shaft.(Its best to never remove the gear from the shaft unless absolutely necessary). If the tabs are damaged, it can allow the gear to become dislodged upon start up. It's always best to replace both the governor gear and the governor gear shaft together if there is ever a governor gear failure because the little groove in the governor gear shaft can be worn which could cause damage to the governor gear itself. Before removing the governor gear shaft from the case. measure the height of the shaft from where it protrudes from the case and install the new shaft at the same height making sure the little groove in the governor gear shaft is at the same height also. I always replaced the button that goes in the center of the governor gear also and I always put a little JB weld on the gear shaft where it fits in the hole in the case. Like has been stated, if there is no resistance on the governor arm when the engine is running, the gear isn't doing anything and is probably dislodged? I do it this way because I have learned it the hard way.

Those are some great pointers for when I get around to replacing the gear. I've got about 2 more hours of mowing that really needs to get done. After that I'll pull the engine and drop the pan to see what happened in there.

Well the mystery of the WOT wasn't solved by pulling the pan. I opened it up Saturday and the governor gear looked OK. The weights rise when I spin the gear with no binding of the plunger as I would think it should. The shaft that goes to the lever was undamaged. It should have worked when I had it adjusted. I ordered some new springs for the lever and the one that goes on the throttle shaft itself and I'm hoping that will fix it. Without the governor working, it's a bit of a pain to vary the engine speed just right while mowing.

I got it all back together with new springs today and it runs great. It idles fine and I can adjust the engine speed with no more issues. It looks like it just needed a new spring.
Now i have a new problem. The POS won't move and the belts are the way they should be. Time for another new thread.

The running great was short lived. After I took care of the transaxle issue I raised the engine speed a little and the rpms went super high with no control again. I hooked up a counter spring so I could at least mow again.
I got most of the mowing done but the battery crapped out. It just quit on me. No click no nothing. There was an odd smell and I noticed the battery sounded like it was boiling. What else will go wrong next?

"Super high rpm" probably fried something in the voltage regulation circuit. Your battery probably got cooked from receiving full alternator voltage.

I immediately shut it off when the rpms went out of control again. I was able to control the rpms after I added a counter spring to the governor lever. I was moving at moderate speed when the battery fried. The battery was 9 years old so maybe it shorted out or something. If not then did something in the charging circuit go crazy?

You'll know when you fire it up again. Check the voltage at the battery then check again with it running. If it's much over 14-15 volts, you'll cook another battery if you run it very long.

That's all I need is another problem. I can't figure how an overcharging issue can develop. I had a motorcycle many years ago that had the same issue but I never investigated it since I always used the kickstarter and didn't rely on its lights.

Since you mention motorcycles, it was common for old Triumph Thunderbird or Bonneville motorcycles to blow the headlight if you over revved it.

Voltage spikes are not good for electrical components and one time can do it.