Its bad connections 99,9% of the time. The hours waiting is not doing anything. Its just randomly getting a poor connection back later on.
Don't get me wrong though, controller could be toast, or throttle, so after you go through the wiring very closely, if it does not fix it, start doing some diagnostic tests.
First one may be bypassing the throttle. With the wheel off the ground, try connecting the two positive throttle wires. Three wires, + and - in, and + back out. Somehow short the two +, and the bike will run if your problem is just the throttle. ( or its plug)
Second one, does the motor resist hard when you turn the wheel by hand either way? It might resist some but I mean hard. If it does, unplug the motor wires. If the resistance goes away, your controller is blown. Controllers can fail for other reasons though. But a blown fet on the power wires is easy to diagnose. If the hard resistance does not go away, the motor is melted down, or mabye rusted to the point it cant turn.