Well, it's impossible to say with certainty, since you're not providing specific details, or pictures. Did you remove the kick start lever when you removed the engine from the frame? If so, it must be installed far enough onto the shaft so the retaining bolt aligns into the groove on the shaft. Perhaps your lever is spinning on the shaft and not rotating it?
Some decent close up pictures of the kick start lever, face on and from the rear with the leg deployed.