Awe, that's too bad right out of the box and ya got a problem
I can see the kill switch wire can be spliced, So that's no big deal.
All's I can think of why you thought the threads were messed up, is because the wrong studs were sent to you in the kit with the wrong thread pitch. You didn't know better and crammed the studs in the hole and now their stuck.
It's really not your fault. Call the place where ya bought the kit and explain to them that they gave you the wrong studs with the wrong thread pitch and now you have ruined your motor. They might send ya new motor
They should, where did ya buy the kit?
Or did ya try to re tap the threads and made em crooked? What did you mean you "sorta fixed the threads"?