I am a bit confused about your story. When did the chain break? Just before you stopped?
Anyway, The clutch "goo" you saw was most likely motor oil. The pin you saw was probably the end of your clutch pushrod. The rubber strap, I dont know, but could have been the pushrod oil seal.
When the chain broke is relavent to the story. On those bikes, the clutch pushrod is in the direct path of the chain, when the chain breaks it breaks that rod 99% of the time. I doubt the pushrod could have broken or even been damaged in a stationary tip over, as it is protected by the front sprocket cover.
The good news is that it is a pretty simple fix and shouldnt be too expensive. Let me know if you need any help.
The bad news is there are other critical parts in the path of that chain. Definitely check out your water pump for leaks.
A sad design by yamaha. graemlins/nonono.gif