A few things bugging me...rich idle, residue

I believe you are having "degenerate coil syndrome" and your coils are suffering from engine heat. Getting less spark, running richer close to fouling plugs, but sometimes the complete opposite, and effecting idle. I would bench check the coils and leads and then hook it up and tape the meter to the tank to monitor the resistance on a multi speed/rpm ride. This condition is what a consider a ghost chase if you begin to adjust other things. If the bike was running great before the problem, chances are 1 thing is no longer right. If you make adjustments and they don't pan out, make sure to put them back before moving on to the next item on the list.

My second place to look would be a going bad EI effecting timing.

Depending on the severity of rust in a tank. If it's moderate to light, surface flashing. There is a product called Evapo-Rust that sells for $22/gallon. Just pour the entire gallon in, let it sit for an hour, shake it around, position the tank differently and repeat 2-200 times depending on how much rust needs removing. The stuff is eco-friendly and reusable. Afterwards rinse with gas and fill the tank - done. It works so well that is you drop a part into the liquid the rust is gone by the next day (depending on the metal and amount of rust damage).

Acid etching then needs to be coated, if the rust returns you need to remove the coating - not going to happen.

This guy has some good points.
Steve
www.amckayltd.com/vm34-36.pdf

The vinegar worked very well. I had to use 4 gallons of apple cider vinegar and 6000 BB's. I let it sit for about a week. Emptied the vinegar, rinsed with water, fogged with WD40 and spent another 30 minutes trying to get the final few BB's out. It seems the rust is all gone. I also cut my petcock down and reran some fuel lines, which was a PITA.

What do I need to do to test the coils? It seems those plugs look good yes? I was thinking of putting new plugs in as well since that is cheap.

I checked my valve clearance yesterday, all four of my intake valves are too narrow. I cannot even get a .038mm feeler in them. My exhaust valves are good 2, 3, and 4, but exhaust 1 is over .128mm so I'll have to get a bigger shim for that one and smaller for the intakes. Anyone have a good source on shims?