I had the same problem with mine a couple years back. A couple things to look at is the seat switch. Make sure harness doesn't have a short. Also once I pressure washed the tractor and got to close to the fuel filter and somehow water got up into the line. I was trucking down the driveway and made it about half way it it spit and sputtered until it died. I ended up taking off what looked like a bleeder screw on the injection pump and cranked it over flushing the pump it she started back up.
After changing your filter, when you turned the petcock back on did the bowl fill back up?