400ex transmission issue?

I recently replaced my center gasket so i split the cases obviously. When i put the lower end back on, the output shaft( the splined shaft where the front sprocket goes on doesn’t spin, i can turn the transmission if i rotate the crank,(the bolt behind the timing cap. Before i took it apart it spun freely. Does it have to work its way into the seal when it spins. I just dont want to put the engine back in and the tranny doesn’t work. It seems to shift fine.