I swear, every time I see crap like ^ that I want to strangle somebody. It's YOUR bike. YOUR vision and YOUR masterpiece. Do what YOU want with it, don't let anybody tell you that you shouldn't. Some people feel the need to go above and beyond constructive criticism and start bashing. I wish somebody would call my modified airhead a shitheap to my face...I feel better now lol.
Now to address what you've been asking, I need to ask you something, how radical to you want to get with this? As for your master, you could go OEM BMW with integrated handlebar controls. For your single disc set up, I'd go with a 12 or 13 mm master, look on ebay for them. Or if you're not happy with your brake performance, you could easily get another fork bottom with the ATE caliper mount and go for dual discs. I'm actually looking at going a step further and not only upgrading my master to a newer Brembo radial master, but adding a second disc and fitting 4 pot oilhead calipers or even some 6 pot Tokicos. You can find the stock masters on motobins here http://www.motobins.co.uk/bmw-parts....20valve%20Twin
go to Handlebars & Levers/Assemblies.
And personally, I've never really cleaned my cases to the point of getting them blasted. I've used alot of engine degreasers and cleaners that do quite the job. Thing is, I feel like when the engine and trans get blasted, they look awesome, but they can be two different shades of aluminum where if they're just really clean, they have the same shade of almost clean. If I were so inclined, I'd get them bead blasted.
As for your ignition, you can stick to stock points, or go electronic with Dyna III. Even going for Dyna coils would be an improvement.
Good luck man, keep the questions coming and the knowledge flowing!