You should install an inline spark tester on that cylinder to verify if you have spark when this occurs. You could have an intake manifold leak which can cause a cylinder to drop out. Have you pulled the spark plug to see what it looks like? Here is a link to the service manual for your engine. There are troubleshooting charts as well
http://www.kohlerengines.com/engines/onlinecatalog/pdf/sm_24_690_06.pdf

 

I do have the svc manual already. I will get a spark tester and report back. Thank you!

 

Finally had some time to throw at this.

At this point I'm thinking coil.

Although the left cyclinder seemed to lose spark more often, the right would also do it. Pulling the plug wires off the offending cylinder for a few seconds then putting it back on fixes the problem. Almost like the coil is getting hot trying to drive 2 spark plugs and pulling the offending wire lets it rest a bit and replacing it on the plug it start sparking again immediately.

I inspected the wires and they look good. I think I'm going to throw new plugs in and see if that changes anything.

 

Rotate the plugs and see if it follows a possibly bad plug. It may still be on one cylinder at full throttle just not noticable. Like Walker said check for spark. Most likely a bad coil.

 

Not sure if you saw the update I posted immediately above your response. Without rotating plugs it already switches back and forth between sides that are missing but left side does it more often.

 

Only items that control spark is flywheel (magnet), coils, wiring and plugs. Would take a look at flywheel and wiring to make sure nothing is going to ground (may happen after heat or vibration) if that checks ok change out coils.