So all in all, its sounding like I will be tearing into the engine a bit..
The rest of that dowel is probably ferrous metal and it's in there some where.I like the magnet idea. If there is any more clutch plate, it won't help with that since they're aluminum, but still probably a good idea just for anything else. I think I will throw the new filter on, get some fresh oil in there, put it all back together, and fire it up and see how bad the sound is yet. If I get ambitious while I am waiting for the clutch to show up, I might take a stab at pulling the valve cover off. I had an 2003 R1 before that I got pretty damn good at pulling the throttle bodies off to get to the valve cover and did the valve adjustment, but this looks to be a little more intensive than the older one. I am still confident I could do it, I will just have to take it a little slower and more precautious.
I thought the write up in the service manual for disassembly was pretty good. Occasionally you get a set of instructions like 'remove motor' and the 'to install motor reverse order', but, does the manual really have to hold your hand the whole way?New update. Got the new clutch in and everything put back together. I notice it will still make noise, but the noise goes away at idle when its all warmed up. See the video, don't mind the slight ticking, I don't have the headers on all the way. But you can still definitely hear the noise. I also rode it around the apartments quick, and notice that it doesn't make the noise when there is load on the engine revving up. When you let off, the noise presents itself. That reminds me of chain like behavior...The cam chain is nice and tight with a brand new cct with the blue dot on it. I'm mentally preparing myself for taking the engine apart, but wanted to just do one last check in case there is any possibility it could be something else. Does anyone know of any good write ups for disassembling an engine?