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)
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.