I bought the bike 4000 miles ago, no way it was ever there since I got it. I have cleaned up the primary cover and no sign of the bolt, nor is there any sign of it on the primary cover of it working its way out, so I truly believe it was not there from the last time it was worked on. However, I am still uncertain of it causing the throw out bearing failure or causing any other havoc in there. The clutch has worked flawlessly for the last 4000 miles and I think a new bolt, a new push rod, a new bearing, a new gasket, new oil, and properly put back together, the bike will be good to go again.
The main reason for my worry was that it felt just like the clutch cable broke but the way it broke was just wrong and the ends didn't match up. The bearing the way it was makes perfect sense as to why the clutch handle stayed in and why it made the squeak it did. I talked to Matt at Baker before I started wrenching and he was VERY helpful. However, he also thought it was just the cable. I will call him again tomorrow and order a new bearing as well as the other parts needed to get it right again.
Thanks for all inputs, it is very helpful and gives me a ton of ideas as what to check and what not....