After some weeks I found some time and started to disassemble the whole bike.
After removal, the engine was opened and split (unfortunately there are not much pictures available of that)
Gearbox 
Clutch 
Geabox 
Cylinders 
Worn Cylinder Coating 
Worn Cylinder Coating 
Crankshaft 
Crankshaft
I sent the cylinders and the crankshaft to a company called MuS Förster to have them checked. According to him, the crankshaft and all bearings are still in very good condition, so it will only be re-balanced. The cylinders, on the other hand, both have different dimensions, which is due to a defective cat of the exhaust system. So the cylinders are recoated, which costs 215 € per cylinder.