I tried a new thermostat, changed oil and filter, bought new air filters and a fuel filter. It takes over 40 minutes before it will start again... any solutions?

Hi,
It could be a number of things. Examine the glass bowl where the fuel filter is to see that it remains full; I think it probably does since other problems would also happen. Disconnect the inlet to it an turn switch on to make sure pump in tank works. You could try loosening the fill cap as well.
My guess is that the fuel shutoff solenoid is overheating and shutting off the fuel. It is mounted on the side of the engine and has three wires going to it, probably white, red and black. It has two circuits in it, one is the pull-off to activate it and the hold-off to keep it open. Properly adjusted, it will have about 1/4" of non-movement in it. This keeps it from overheating. If it does it will drop out and shut down the fuel and engine until it cools. It will also cause it to fail eventually. On that is failing can also do this.
It is the piece that makes a "clack" when the switch is first turned on. Find it and see how it appears when machine operates and compare when it shuts down. You can physically activate it to verify.
Peace,
Clarke