Spent a fair bit of time working last night and I am proud to say.
IT'S DONE!There will always be little paint touch ups and tweeking to make it more rideable but the goals I set out to make it rideable with a cafe look are done.
The side covers were the last major thing to do. Had I just taken out the airbox I wouldn't have had to make a different set. That being said I did have a set of side covers for it but they are very curved and swoopy and I wanted a boxier look. I made a cardboard template then cut it out in checkered aluminum.

When I cut them out I put the future 90 degreed curve on an existing 45 degree curve on the aluminum. This made getting a nicer sharper edge way easier. I put two folds in and riveted them together.

Here they are mounted. Right now it's just tie wire holding them on but I may end up welding a nut or two on the frame and running some bolts through. I like the tool free ease of tie wire for getting them off.

I am not really digging the look yet but the black paint dulls after a bit of time and that should help draw my eye away from them. They are larger than the old ones and super boxy which was the look I was shooting for but I got more box that I was expecting. The left side cover needs a rubber/plastic flat on it on the front to keep the water from getting into the fuses etc. The other side seems to fit and cover everything well. I was thinking to break up the look a bit I could paint a racing number on the side or something else to break up that big flat area. Open to suggestions.

I bled the brakes, strapped some loose cables to the body, removed the horn, put passenger pegs on, put in cotter pins, mounted the license plate and cleaned up a few spots.
I was thinking about mounting the license plate like this

but I was unsure about the legality (I worry to much for a future cafe rider) I know you are supposed to have a light on it which would not be hard to do but does anyone know if there are any legal issues with having it low and sideways?
I need to find a little horn and mount my tool kit somewhere but man it feels good to be done. Now to get my other 3 CM 400's running well.
I will get back up there and take some non ipod quality pictures to show it off a bit better.