UPDATE:
So, I took the carbs off and cleaned them (they needed to be cleaned anyways)...
Then I had this random idea. Perhaps, my problem was ignition because it was happening under the most load (resistance at low rpm). So I installed 4 new spark plugs and reinstalled the newly cleaned carbs.
The bike started up well and I took it for a spin and it seemed like my problem was fixed.. a lot of the power I originally had was back (if not all - it was hard to tell). I then realized thought that the engine sounded a bit funny so I tested the ignition coils and realized that only 3 of the 4 cylinders were actually sparking. It seems my wires had gone bad because that fourth one was shorting out before it reached the cylinder. I'm going to pick up new wires tomorrow (and pods so I can get rid off my filthy airbox) and give an update.
But the good news is that the bike runs!!
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