They are rock solid bikes, but still a bit quirky. Ride it and don't worry if it vibrates or makes more noises than your Honda.
No one is snapping belts because of stock power levels. XB9 and XB 12 HP is surprisingly close. the belt doesn't even have a maintenance schedule. I'd replace it at 30k though...
the breather re-route is meant to keep the intake cleaner, go ahead, and make sure to plug the holes left in the airbox when you pull them out.
Keep it stock, or get a muffler of your choice and match the ECM program to it. You can buy an ECM from IDS, or check out Buelltooth.com for options.
You can get a service manual from there as well, or Buellmods.com
Head gaskets are NOT a maintenance item. Did he mean rocker box gaskets? If so, take a close look at the fan. If it's oily I suggest replacing it before it dies.
Good idea to change the oil anyway, that way you know for sure. You shouldn't have to be inside the primary for much? Primary oil changes, clutch adjustments and chain adjustments are all done externally.
The Gel battery is fine however you like it.
Don't let the fact that its air cooled frighten you. Lots of testing went into component location and function, you aren't going to make it better. Air cooled engines are VERY robust. You'll absolutley know if it's overheating. The ECM will retard timing, lower redline...Pinging, knocking, lack of power, etc. Just pull over when you can safely and be patient. That said, I spent a LOT of time in Florida (100 ambient) on an XB and never had an issue, even flogging it at the track.
The flat spot was most likely caused by the air horn gasket being out of place, pretty common, good on ya for finding and fixing it.
Whenever you feel like working on it, wash it, ride it, and park it again. It's better than looking for problems that don't exist
Welcome to the forum. Hang out, be positive, share info, and Post pics!