I am leaning toward a faulty EFI pump. Also keep in mind there is also a filter inside of the EFI pump that is non serviceable, and will clog if the wrong inlet fuel filter has been installed. If I remember correctly the internal filter is a 10 micron, and they recommend a 2 micron inlet filter on the Kohler engine.
There was a case of if I remember correctly it was an older CH26 that would run great for awhile and then loose power and throw engine codes. After running for like an hour the fuel pressure was dropping from 43 psi to 13 psi.