IMHO. I would replace the Doohicky first. The Doo can frag and end all happyness, without warning. I'd address that. If you have not looked into the Thermo Bob, at least study up on it, so you will know why heat warped your cylinder, giving you the opportunity to know first hand where you can get the best deal on gallon jugs of oil, 'cuz that's how you will be using it...by the gallons. I'm not much on after market exhaust, if modifications with the stock exhaust net some positive results.
I try to keep the whole farkle thing in some kind of perspective. If I had a race horse, should I focus on what color and kind of stable blanket it would look best in, or what colors the jockey would look best in, or should I first make sure the nag is fit and in shape to run before I sink one flat dime in how it looks?
You've heard it before, and in this case, it has real meaning: "Chrome won't get'cha home"
Your farkle list is very reasonable. I would just get some priority to it. Do as much of the mechanical and electrical modifications done as you can, as soon as you can. Eagle Mike for the doo. You may run into a snag installing it, and the crisis intervention that comes with the kit is worth twice what you would pay for the doo. If I were in your shoes, I would be looking for or start making noise about a tech day in your area. In case you are not familiar with all that, thats where a bunch of riders get together and wrench on each others bikes. Those who can wrench, do. Those who can't, better be good cooks and know how to stock the beer cooler. Good place for ideas, horse trading, and information that money just don't buy. I'm in kindergarden with all this, too. I put about 18,000 miles on a KLR last year. I wouldn't be able to do this much tweaking on most other bikes. Couldn't afford it, or have the skills / tools to do all that can be done on these bikes. With nothing more than a driveway, the local Walmart and a Goodwill Store, you can rebuild one of these things.