500 ninja flywheel?

Question

When I pulled the flywheel, I noticed there where a bunch of magnets missing is this the reason the battery wont stay charged?

Answer 1

YES!
Also if some magnets were missing, they had to go somewhere. Are you sure the stator isn't damaged? If someone had the bike before you, the magnets probably came off the flywheel and wrecked the stator. He cleaned everything up and put it back together for the next owner to worry about. Every part of the charging system should now be checked out.