I have no power output from a MegaForce 6500 Generator. I get a reading of 5 volts when checking the positive lead to ground. I have read that the generator may need to be flashed and looking to find out how to do this to this generator.

Don't bother, just get a battery and repolarize your capacitor. Tap the pos to pos and neg to neg for a second or 2 them reattach the leads and see if it starts making power. A 9 to 12 volt battery will work ok for this.
If it wont take the charge, just get a new cap. The original capacitors are pretty cheap anyway.