Nice bike, wish mine were that clean! Maybe someday...
Anyways, Those holes in the bottom will not be enough to seriously throw anything off. They were caused by 1 of 2 things though. Some dumbass tightening the bolts WAY too much or by a person who cross threaded the bolts and kept trying to tighten.
See these bottoms are not meant to turn, the plastic holds them so you do not need a second wrench. People end up stripping them cause they think they need to be super tight and that isn't the case.
I ALWAYS split my airbox when I take it out. It is so much easier than as 1 unit. I used to do that so, I know.
Use a resin of some sort to fill the holes and hold the bolts and you should be fine there.
What sort of fuel issues are you having? I assume this isn't your first bike so we would need to know what your other bike was for comparison purposes.
The ride IS the adventure. The destination is just to get gas!