I'll do the big one first.....raising the frame! I did my bike last winter without raising the frame, you can get the same action just by lowering the motor. I used jackstands at the foot pegs area and a small hydraulic floor jack under the engine. Would I do that again ? NO!!!!
Besides the safety aspect
it causes too much crouching for my old(er) back and knees and the stands are always in the way. But later on I found out that I could have put a steel bar across and through the peg mounts and install the jackstands at the ends of that bar, away from the bike. But you cannot do that right at first because the right mount has to come off in order to remove the shock lower bolt. You can also do something similar if you leave the rear frame/tail piece on, 4 x 4 across and set it down on some sturdy sawhorses, but not easy to work around those. But remember safety first....!
Special tools like the clutch centering tool and clutch holder, if you mean the one to hold the parts centered.......I did not use any of that, there is ways around them all.Even the big socket with a window cut in it....I bought one, used it but never cut it !
I don't know about your clutch parts, would really have to see it, depends a lot on how long and how much the clutch slipped, I got caught once not replacing the diaphragm spring, but the plate/housing cover are quite resillient, they may only need a good sanding and cleaning.
Buying parts before is a good thing sometimes, makes you feel like it is X-mas for the bike, but I'll bet you'll get a little jam or two and have to get more, so you may want to wait until you pull the clutch out and inspect everything until you finalize it all.
Have to edit....Why the pushrod? My bike is 2003 and does have the updated one with the felt on it. You can also drill a weephole there if you are concerned about the potential fluid leaking out of the slave into the bellhousing.That's why I said inspect first, you may not need that, but even if you do, it would be no problem machining one that does not have the groove and install the cheap felt on it. I do have the specs if you need to do that, I carefully measured mine so maybe someday I could save someone $50.00...