I went to test the pull and something was causing a major clunk. So I pulled the cover and cowl off yet again and saw that the magnets on the flywheel were hitting the e-coil, which I didn't think could move, but sure enough they had just a couple millimetres of play when I loosened the bolts. I tightened the bolts with a gap enough for the magnets to pass by. The last thing to attach was the new cutting blades. I was really happy that she started first go and gave it a little test mow. Worked just fine, if not a little fast on the revs, but I can adjust that on the carby. All in all I'm pretty happy with the result and proud of myself for accomplishing this project. Thanks for all the advice guys.
Video of it running
Mowing Test