2002 Kohler 25hp Command Vertical Shaft Issues

The SAM and the modules should have a part number on them. That may assist is looking up parts and/or bulletins relative to your engine.
I did some deeper cleaning and did find Kohler numbers etched in the SAM 24 584 09 REVD 01065 . Piecing the numbers from the coils together they are 24-584-15 00235.
 
The symptoms you described sound like a fuel issue. Trash in the fuel tank is getting sloshed around and finally clogging the pickup tube. Waiting a while and the trash settles. Start mowing again and the symptoms repeat.
It will do the same thing off of either tank, both of which have no notable debris. I have a new filter with nothing showing up in it. I have not replaced the fuel lines which are original and have some pretty long runs but appear to get very good fuel flow. Honestly have not taken down the carb and cleaned it, not sure if could be some fiber/lint in the mesh somewhere. With all the bad press on the SAMS and coils from the era and the location near/above the exhaust thought heating up and shorting/faulting makes the most sense, just not accustomed to such a investment to rule out ignition. I will focus on the fuel as well.
 
It will do the same thing off of either tank, both of which have no notable debris. I have a new filter with nothing showing up in it. I have not replaced the fuel lines which are original and have some pretty long runs but appear to get very good fuel flow. Honestly have not taken down the carb and cleaned it, not sure if could be some fiber/lint in the mesh somewhere. With all the bad press on the SAMS and coils from the era and the location near/above the exhaust thought heating up and shorting/faulting makes the most sense, just not accustomed to such a investment to rule out ignition. I will focus on the fuel as well.
New fuel lines are fairly cheap.
 
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