Hi Justin, welcome to the forum!
Mechanically, you can swap a 2001+ stator into your engine by swapping the flywheel, and left side cover/stator. That is how I transplanted a 2000 TTR225 engine into a 2007 TW. I am not sure if your 1989 CDI would work or if you would need the newer CDI and/or other electrical changes.
Is the bike running at all? The reason I ask is because others have replaced coils, stators, etc., only to find that they were not the problem. Unfortunately, I can't offer you much electrical assistance.