whenever anything is being stubborn to come out, I find that a little wd40 and hammer the piss out of it goes a long way! Sometimes all it need is a good pounding on the casing to knock it loose. Use a rubber mallet of course. I'll also put the rubber mallet in place and hit it with a mini sledge hammer aswell for some good force. When I bought my used quad it was trashed, the swingarm bearings were completly worn, nothing but bits.The outer case to the bearings were literally welded in the swingarm. I picked up a near new swingarm for $25 on ebay.
the repair manual I have suggested letting the nut on, but not tightened all the way, then putting a socket over the nut and hitting the socket with a hammer. My swingarm bolt came out easy, but that's the method I used when I removed the axle and it worked good