For future reference you have use a 3 point puller to remove the flywheel from what I can see of the flywheel. Here I use a harmonic balancer puller and brass hammer. I mount the puller, tighten up the slack plus a little extra tension smack the center puller bolt to jar the flywheel loose. Sometimes it might a couple retighting of the center bolt to get a good jar to loosen the flywheel.
As for the flared crankshaft end file it back down so the nut slips back over it and that starter doesn't hang it.
Muffler are something tends to rust from the inside out so a replacement would be better.
