23 HP Kohler Command running rough

Hi guys Luke Routh here, new to this forum. So I have a very long story on a walker lawn mower that im going to make as short as possible. We bought the mower probably 8-10 years ago and a year or so after the original mower through a rod and was replaced with a brand new Kohler Command 23 hp because it was a cheaper replacement that the original 20 hp. After 3 years or so we started noticing this new motor was smoking slightly and would foul a plug. The motor also seemed to have a light skip/pop on one cylinder and didn't seem to have the power it should. I checked compression and leak down on the motor and all seemed fine, but curious if it could have been a bad head gasket and to visually see the inside of the cylinder walls I pulled the motor and pulled the heads. All seemed to be good and you could still see the etching marks from where it was honed from factory and no noticeable scoring on the cylinders. Re installed the heads and motor and same thing, a little bit of a skip on one cylinder and smoking just gradually. I have tried cleaning the carburetor thinking that maybe if it was a "double barrel carburetor" like some i have seen that one cylinder just wasn't getting adequate fuel. I have also tried new plugs, setting the valve clearances, etc etc..... I am at a loss for what it could be. The motor literally has maybe 200 hours on it and unless a ring is broke im at a loss. Is there anything else anyone can think of for me to try to diagnose this? Fast forward about 3 years of it sitting in the woods, I needed to get leaves up at a newly purchased property and my dad said I could basically have the mower if I got it out of his way so I dug it out, cleaned the gas tank out, cleaned the carburetor, replaced the fuel filter, checked the fluid and greased everything and got it running and mowing. After mowing for 45 minutes or so it seemed to be doing fairly decent, other than the partial skip or pop on that cylinder. I got a stick hung in the grass catch chute and clogged the pipe tight with grass to the point it was putting a heavy load on the blower/motor and the motor wouldn't hardly pull it. I cut the deck off and noticed the exhaust for the cylinder closes to me was red hot and the other cylinder was not. Any help is greatly appreciated because I really hate for that nice of a mower to have these issues. Thanks!