It does sound like she has a bottle preference. It happens. If you have an overactive letdown then she would prefer the bottle because it comes out in one smooth flow without choking her.
What to do? Pump off the initial overflow and then nurse her. Stop bottles altogether? I know that would be difficult because you are worried that she isn't getting enough milk. But if she prefers the bottle, she is going to cry for the bottle, ya know? I've had babies cry for the breast when I offered the bottle. THey preferred the breast and wanted that. It works both ways unfortunately.
As far as fussiness goes... I'm not thinking it's your milk, if she isn't fussy after drinking a bottle of your milk. Gas from gulping too much air?
That all said....my oldest was like this. It took us 14 days to get him to even latch to the breast and then it was FUSS, FUSS, FUSS on the breast. IT wasn't my diet. It may or not have been overactive letdown. I'm not sure. I was a new mom and didn't have many resources to help me. Unfortunately, or fortunately, he wouldn't take the bottle either. Around 3 months old, he started doing better and we went on to nurse for 3 years
Oh, one thing that I did a lot was pick him out of a sleep and nurse him. He was half asleep and he'd take the breast better that way for some reason.
Good luck momma.....I can feel your desperation and I am really hoping that this all resolves quickly for you. HUGS!