I'm a lousy mechanic but I don't see any mention of checking the fuel filter?
Maybe just coincidence but with a near empty tank and then fill maybe some gunk on the bottom of the tank got stirred up and migrated to the fuel pick up and is blocking fuel to the engine?
Like I said though, I'm a pretty lousy mechanic especially when it comes to diagnosing problems.
One more thought...How is your battery? On my 40 I was getting some 'surging' in 4th gear like the engine wanted to die and wouldn't put out full power. Dinked with the carb and all sorts of stuff but couldn't figure it out. Later (I don't drive it much) I replaced the battery 'cuz it was dead and I've haven't noticed the surging or lack of power since....
Oh, and if you get in a bind and need a vehicle for a few days, my 40 could certainly benefit being driven