xb9s running rough?

[beer0060]

just bought an 03 xb9s, its my second bike (05 SV650), this if far better and i am having some problems with either fuel or intake. shes running pretty rough off the get go and it seems like its not getting enough air to the engine but it could be because i put regular 87 gas in on my first fill up. i got a tune up and they dont even know why this is happening. since the bad gas ive been putting 91 octane plus some octane booster, and i dont know how many tanks this should take to pass over but im beginning to think theres something else going on. when i first drove it off after buying it like a week and a half ago it ran great. anything as for advice or info? shes hurt and needs some help thanks.
charlie

[JSW07]

I'd say get a TPS reset then try riding keeping the rpm above 3000rpm (seems to be where the ECM starts learning) to help the ECM learn the mapping for about 10min, see if that makes a difference.