What are steps to align clutch after motor swap on skidoo snowmobile?

you need to get a clutch alignment tool for the specific brand and set up you are using, it is usually a tool that drops over your primary clutch and slide just past the inner edge of the secondary clutch. (sort of looks like a flat "Z" shape hard to explain) Most manufactures want there engines to be twisted towards the front left shock (sitting on the machine) so that when the engine accelerates the clutches line up and the belt is straight. You will also need to measure the center to center distance as in the center of the primary clutch to the secondary clutch the is a spec for this for each manufacture. If your not exploding drive belts all the time the clutches are probably aligned in an acceptable way. If you are going through a lot of belts you should check the condition of your clutch for wear and if both are in good condition then do the alignment procedures.