All the fuses are intact and the clips are in fair shape. As soon as this happened I checked them and they were fine. Is there anything else I can check for? Is it even possible to short out a harness?
That's pretty rare, and doesn't usually happen instantly unless there was prior serious damage.
From your description, the only part of the circuit I can think of that might have gotten really heated would have been the Green ground wire. This current path would have been from the terminal of the (+) battery, through the Red cable on that solenoid you hit the frame with, to the frame, then to the engine, to the Black ground cable, and back to the battery. The little Green ground wire underneath the seat lock bracket would have shared some of this current, too.
My next thought: check the battery voltage with a meter. Some of the cheap Chinese batteries we are seeing these days could potentially melt their internal busbar connections from such a high-current short. I have seen the insides of these batteries (Bikemaster comes to mind), and they are poorly cast and constructed. The Yuasa batteries are far better, and are made of purer lead, which will WAY outperform the Bikemasters I have used lately. :-/
