Try this for troubleshooting.
1. Remove all wires from the + side of the coil
2. temporarily run a jumper from + battery post to + on the coil, and start it
3. disconnect the wire from step 2. It should shut off.
assuming that works fine, do you have any other wires on the switched side of the ig. switch? I am assuming that feeds part of your fuse box. Isolate the wire going from the key switch to + coil (may need to temporarily run a new one) and make sure it starts and stops correctly.
I think your generator output is feeding back through the switched side of your fuse box.
