Spray carb cleaner around the rubber carb boots at idle to see if there is a vacuum leak.
What color are the spark plugs?
Have you tried to adjust the mixture screws?
Turn each in until the engine starts to slow down then back out 1/2 to 1 turn.

 

Thanks! I did set my mixture screws when I got the bike 6ish years ago, but I will try messing with the mixture screws and testing for vacuum leak tomorrow morning. The plugs were a bit carboned up when I pulled them, so my guess is running a tad bit rich, but other than that the gaps were within spec. Although, I have never changed them before, so I'm not sure how old they were.

 

Is it stock air filter and stock exhaust? I would check air flow (filter/obstruction).

 

Air filter and exhaust are all stock, and when I put the seat on I made sure to not obstruct the air flow. It was just super weird that it lost power while cruising at low speed. Im going to check the vacuum possibility right now, suggested by swifty.

 

So today I checked for a vacuum leak around the carbs; all seemed well. Before I checked the mixture screws, I decided to double check that both cylinders were firing. It seems that I am running on one cylinder as one pipe was uncomfortably hot and the other was only warm. So now at least it's down to one side of the engine, with the most notable symptomatic cause being a random cut out while cruising after running 100% normally. I will start checking my hoses to make sure nothing is kinked, and will go from there.

 

So I came across something interesting today. I had the seat off and something possessed me to wiggle the wire harness while the bike was running. when I did so, all of a sudden it pepped up to 1200 rpm (where I had set it before) and my rear cylinder started to fire/lost its weak spark. Thought I'd share my weird revelation with you all today. I will be going through and tracking down the wires that have anything to do with ignition.

 

The wiggle test has proven valuable many times.
Go to the ICU and gently tug on each wire and see if it reacts.