I'm wraping up the replacement of a 01kx250 linkage as I write this. I made a bearing press out of a lag bolt and nut, coupled with various sized sockets and washers. Just press out the old ones and press in the new. Good luck with it.
I had a problem getting the pivot bolt out too. All I did was go to Sears and bought a small sledge hammer and a big punch. Problem solved. I imagine that by doing it my way, you can ruin the bolt (by mushrooming out the end, or screwing up the threads) so be careful.
It might not be so easy. It depends on how badly the bushings or bearing races have gotten grooved. If they are badly grooved, you are going to need a BIG hammer and will probably ruin the swingarm bolt, which costs about $21. If this sounds like the voice of experience, it is. I learned my lession and now make sure I disasemble and lube the swingarm bearings every year.
When you drive the bolt out there is a simple way to hit it a little ways with a sledge without hurting the threads. The thing to do is put the nut on a little ways and hit as hard as you want. It wont tear the threads up. Won't hurt the nut very much either.