My wiring harness shorted out after my license plate bracket got ripped out and the grounded over head light wire touched frame. It shorted all the way to my ignition and when I got a new wiring harness my bike turned on but would not turn off. I don't think the problem is the kill switch or kickstand. But what ignition can I get that would work with the 2001 savage wiring harness

The stock wiring harness has a fuse in it.....I would have expected the fuse to blow when the short occurred.  Do (did) you have the stock tail light and wiring harness in place when the short occurred.

Not sure why your bike would have stayed on when you got a new wiring harness....either you got it hooked up wrong or your switch went bad in the burned wiring event.  The key switch sends the battery power to the ignition system.....that power should go away when the key is turned off.

There is no aftermarket or optional ignition that works with our bike and is a plug in......some folks have adapted other switches including those that are just ON/OFF switches without keys.  There are only 3 wires to be hooked up to the ignition switch....so it is not difficult to adapt something.