Motorcycle Repair: Bad Gas, octane gas, cheap gas

Question
The man I bought my used cycle from suggested that "every so often" he would "run a tank of medium (89)octane" through.  He said it was to "clean up the engine just a little", and that the cycle might "run better" when that was done.

This week, I ran out of gas as I coasted down the final hill and into work. Fortunately, the janitor had a 3-4 gallon can of gasoline left from summertime mowing...and so, he dumped about 3.25 gallons in my cycle.  He said it was the cheapest gas he could find at the time.

Now, I've noticed that my cycle is missing on occasion. Is it more likely the cheap gas, or the fact my tank ran dry on reserve?  And, will it likely improve with a tank of 89 octane?

Answer
All the higher octane gas does is stop pinging or pre detonation, so if you dont have that problem with the lower octane gas then use it.
The gas he gave you might have been old so I would drain it and put in some fresh
Good luck and happy riding
Mike