Don't run the bike. I don't have a manual right in front of me, if I did, I would be looking for any "pins" or "spring pins" or "roll pins". Maybe, a very competent parts guy can help you locate where it might have come from. Once you know where it might have come from, you can then decide whether you have the mechanical skill to repair the bike.
If you run the bike it could cost you *much* more than a minor engine teardown.
If you are unsure of how to repair it, bring the bike (trailer it, don't ride it - unless, you like to gamble...) to a competent Hayabusa mechanic. Pay some now, or pay big later. As it sits now, you will be probably paying for only (my guess) a spring pin and labor (it won't be cheap depending upon where the pin is located).
A related story: My old MX riding buddle was rebuilding the top end of his 125 2-Stroke one day. The wrist pin had needle bearings supporting it. One needle bearing fell out while he was inserting the piston on the connecting rod. He couldn't find it. Didn't know if it fell in the crankcase or not (of course, he didn't stuff a rag in the opening to prevent such a problem). I told him to either find a magnet and use it to see if he could find it in the crankcase, or split the cases to *verify* that it didn't fall in the crankcase. He didn't want to split the cases, so he bought another needle bearing, closed up the top end, and tried to start it. Yep, as you would expect, it started, then immediately froze solid. When he removed the top end he found his "missing" needle bearing (jammed between his piston and exhaust port.) Moral of story: Plan for the worst, expect the improbable. Is the risk worth it?
Maybe one of the other members who have torn down their motors a number of times might have a clue as to where it might have come from...
Good luck.