Bare magnesium is hard to paint without a special primer that is expensive.  Aircraft painters should be familiar with the process.  Painting over the original paint (carefully scuffing without stripping) works also.  If there are any bare areas on the magnesium, expect that the new paint will bubble and come off easily in those spots.

An odd trick I learned back in the late 1970's with my Husqvarna and still use today is to spray magnesium with "Gibbs Brand Lubricant" before painting.  Don't ask me how, but it works.  gibbsbrandlubricant.com/

I got so tired of the paint flaking off my 400 side covers I decided to spray them with truck bed liner. It has held up for several years now. But my bikes are not concerned with stock appearance. I actually like the look of it on this stripped down bike.

imgur.com/a/OrPQLgg

That engine looks pretty good! Maybe i will just give it a try.
Did you use a primer before or just spray over the old paint?

So I didnt got any positive reactions from paint shops but now when I read this, I maybe will paint it by myself.
Unfortunately I cant find any distributors for Gibbs Lubricant in Germany, but I already found a primer for non ferrous metals like aluminium or magnesium. Will ask for a right paint. Then strip down the old paint and use the special primer. In this combination i shouldnt get any trouble with bubbles etc.
I trust your experience, but using a lubricant as a paint primer doesnt sound right, haha.

I did not use primer. I removed the flaking paint, lightly sanded the problem areas and sprayed a couple coats of rustoleum bed liner.

I like the exposed edges of the fins. Very nice looking!

Hey, I have some news.
I had the cylinder and head sandblasted and prepared the engine covers with 400 and 1000 grit sandpaper. I treated the carburetor with paint stripper and sanded it with 1000-grit paper. Then I primed and painted everything with 2K paint for brake calipers.
I masked off the flanks of the cooling fins beforehand so that I also get the effect.
I'm happy with the result, even if it's not quite perfect.
The cylinder is also drilled and bored on the Wössner piston.
Now I have to do some minor finishing work on the paintwork and tomorrow I'll start assembling it.

Some Photos:
imgur.com/a/uCMzy5U

Looks nice.  Hopefully your paint holds on. My paint job lasted over a year but then one day I walked up to the bike and huge flakes had let loose. I could literally flick the paint off with my finger.  Not sure what triggered it to happen after such a long period. 

Hello, A friend powder coated his CT90 cases, covers, head and cylinder. The engine never sealed, still fighting oil leaks. Im not a fan.

CT90's will put up with anything. Just saying.