After a month of fiddling with her, I finally broke down and brought my baby to a shop. The problem that has been plaguing me was that she got super sluggish and bogged down (almost like one cylinder firing inconsistently), then eventually die altogether on lower RPM's. After a while, she would eventually run great all the way through the powerband, only to then sputter out and die 10 minutes later. Waiting a few days would then make her fun again for only 10 minutes, rinse and repeat.
So I brought her to a shop near me. They took apart and cleaned the carbs, fixed some messy work of mine from the rebuild, and said she's good to go! Well if you see me posting on this forum you know things aren't running right.
Now what's happening is above ~30 mph the bike does the exact same thing as before, although now the problem is happening all the time. Very sluggish and bogging down. I immediately brought it back to the shop after picking it up. The theory that the mechanic at the shop gave me was that one of my pod filters was in direct view of the forwards wind, therefor forcing air into that carb. I was unsure, only because I've had 900 miles since the rebuild with pod filters without ANY issues. So I come to you handsome folks once again to beg for help
(I'd like to note that over those 900 miles the bike would become sluggish just like this problem, although it only happened 2-3 times ever. After riding for a while she would begin to bog down. After waiting a minute or two on the side of the road she would start right back up without issues. Almost like the phantom out of gas issue. Now it's become a regular occurrence. I have a new tank that's properly vented btw.)