Sounds like a good plan. Be prepared to shift gears at any time though. I've never seen anyone modify anything without being inspired to make changes to their plan as they progress forward! I have had good experiences with Rick's. Never used a Shorai battery, but I would expect no issues. I have used a few AGM batterys, and they can go haywire if overcharged, but seem to come back unscathed if severely discharged. Stock motor with enhanced electrics is great idea. New exhaust and air cleaners will add a lot, but take a lot more consideration than most people think. Everyone will tell you to get it running and driving perfectly before doing anything, and you will never get better advise. New steering head bearings and swing arm pivot bushings should be first on your list after that. Improve them with tapered rollers in the front and bronze bushings in the swingarm. There is very greatly more to setting up the swingarm than most people seem to think, and it is important. Quality rear shocks would be next on my list. Hands down the absolute best place to spend money on your bike - you get what you pay for and you will notice it. Cartridge emulators and possibly springs for the front forks are another excellent return for the money. Get some decent tires and you will be amazed at how great your bike drives. Now's the time to do all your electrical work. This seems to be pretty fussy for most people, which is why it is a good idea to get the bike driving around well so you can focus on the electrical work exclusively until you get it sorted out. Once you get the electrics in bomb-proof condition, you can deal with the pipes and air cleaners. The improved ignition should help with jetting since you know it is working correctly. Don't know what you have in mind for bars and foot pegs, but my advice is simple. I have bikes that are totally original with the high bars and sit up pegs, and others with clip ons and rears sets - genuine road racers. The most ridden bikes are in between. Low bars but not clip ons, and rear set pegs but more like half way between the typical stock and passenger pegs. Opinions vary! Once you get to this point you can decide on all the cosmetics. Once you do, you can take the whole thing apart and paint the frame, rebuild the wheels and all the rest of that fun stuff you really wanted to do first. But if you save it for last, you can have confidence you will have a beautiful machine that also runs and drives beautifully after you put it all back together. You actually end up with a brand new bike this way. Otherwise, you end up trying to do all that mechanical work on top of all that new paint and shiny metal, and end up with a "used" bike once you get it all sorted out.
Post us lots of pics, and good luck!