This is kind of an open ended question, but...

What projects should be undertaken and in what order?

My main question is can these be done as a 'rolling build', or should I plan a major take down over winter? Here's the list and in the order I was thinking. My main fear is ending up over my head and not being able to get the bike back together or it operating worse than it is now.

1. Replace Muffler / Rejet Carb
2. Install Steel Braid Brake Line
3. Install Seat Loop, Seat, Rear Lights, Rear Fender, License Plate
4. Install low profile tank (done along with above?)
5. Paint (assume this will be needed with new tank)
6. Replace Rear Wheel with 18"/replace tires
7. Rearsets (I really want to do this, but think it's a huge undertaking, so idk)
8. Electrical overhaul (anyone installed a Motogadget m.unit? another wishlist item)
9. Major engine/carb work (Lancer's Carb, Piston, Camshaft)

Completed already:
1. Brake Pads
2. Risers
3. Handlebars
4. Grips
5. Mirrors
6. Headlight
7. Front Springs
8. Shocks

Thoughts?

I think your order is reasonable.  Not far off from what I did.   The rear wheel doesn't have to take long.  I did mine over a weekend when my bike was still stock.  I would probably move it up on the list.  I think the seat, tank, and fender should be done together so that you can make sure you get the lines you want. I think that is probably the most important thing to getting a good look and rear fenders make it harder. I didn't bother messing with the electronics or mechanical items on my bike.  Stock is fine for me.

For me - warm weather is for riding/tinkering and cold weather is for major renovation work.

During the months that are warm enough for riding - I do projects that are quickly done on rainy days, and go riding on sunny days.

I have a nice heated garage and spend a lot of winter days installing new tires, making bodywork changes, painting, engine modifications, etc.

I can't explain how painful it is when I have a bike torn apart on a nice sunny day.......and hear bikes riding past my house!

I'm thinking I'll spend this winter trying to figure out the seat, tank, etc. I like the idea of the m.unit, but think that'll be a later project.

I'm already having trouble with the DRL lights after adding the headlight with LED DRLs. I'd like to convert everything to LEDs, but know there's an issue with reducing the draw and the blinkers. Can anyone explain how to manage that for the front and back? I saw a post that had an adapter picture, but it didn't make sense to me as to what it was exactly and if it would work for both front and rear lights going to LEDs.

It looks like you have the right idea by making a plan first.  The other advice given here by the pros is excellent, listen to these guys!  

As an experienced designer in another field (architecture), I always recommend having a good, clear plan of action for any design project, and this certainly qualifies. Be sure to check out Ohiomoto's build thread, one of the best on here, especially relevant is how he mocked everything up before cutting or welding anything. Post lots of photos and pics, as your project sounds like fun!