1979 Husqvarna 250 wr overhaul

I found the best way to get the kick start into the right position is to take the kick start shaft on the inside of the case and attach vice grips so you can turn the shaft. As you turn the shaft downward against the tension of the spring, you will notice the kick start gear begin to move toward the sproket shaft gear. This is where you will now re-install the kick start onto the splined shaft. Once you have the kick start on the shaft, you can test its operation to make sure in the "rest" position the kick start gear has not begun to move toward the sproket gear. If so, back the kick start one serration back and retry.
Also you mentioned cylindrical marks on the inside of the clutch cover. This is probably caused from using a silicone sealer rather than a gasket and the clutch bolts are rubbing the cover. Purchase a gasket to provide distance from the top of the bolts to the cover surface.
Hope this helps.