Kohler SV620 Will Not Run with Air Filter Installed

I am new to this site, coming here to find an answer to why my Kohler SV620 engine will only start without the air filter installed. The engine failed during a power outage, I called and they sent a tech who said there were several issues including low compression, cracked stepper motor arm, and said it needed a new head gasket and ignition module, plus couple of other parts. It has about 530 running hours.

After replacing the parts, the engine would not start unless you removed the air filters, this was not the case before. We could fidget with the air filter housing and keep it running by not tightening it down all the way. That soon stopped and now I've had to remove the main filter and the pre filter to keep the thing running.

They called Kohler and they have no idea what could be going on. Any suggestions on what direction to go in to get this fixed?