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I wouldn't reuse them, but not because they're oil soaked. Those "spoked" plates have a bad habit of fracturing.
The dark spot don't come off with brake clean, I sanded on disk with a orbital sander and it came off, would it be ok to sand them clean and reuse them or am I worried about getting the surface uneven?
I guess it depends on how much you like tearing down a Spot. That picture of Charlies tells all. Of course you'll get the surface uneven. It might work, though. It also might turn into that picture of Charlies. <shrug> I, personally, wouldn't even consider putting them back in.
Another dumb question, so I am down to rear seal in the motor, do I just pry the old one out and put another in or do I have to pull the carrier to replace the seal?
Consider what Wayne says, of course. If the rear seal *is* leaking, there will be obvious signs of it once you pull the clutch/flywheel. Whenever I have any doubt at all, I put in a new rear seal while I'm there. After all, it's 20 years or so old, and they are cheap. (Guzzi content) I, personally, pull the bearing carrier. No chance of nicking the seal surface that way, and you get to replace the gasket that might be leaking. While you're there... JB weld the cam plug, etc. You *are* planning on keeping this Sport, right? FWIW, a "mechanic" grossly overfilled the transmission in my/Rocker/DRSDave's Lemans 5, and it oiled the clutch plates. When I brought it home, I did the mineral spirits trick to it, and it was fine. That Might have saved you all the hassle.