Engine Install Problem!

ide take a measurement before you pull it apart,,measure from the face of the block,,or bell housing, then pull it apart,, take the clutch and plate off slide the tranny back in to the crank,,with out the clutch,,as far as it will go,, take that measurement,,if it is the same,,your crank, may not be drilled all the way,, or you may have the incorrect pilot bearing or as stated damaged your pilot bearing,,, if the pilot bearing is correct and not damaged,, and the trans input shaft is the pilot bushing most of the way,and you are still bottoming out,,the crank may not be drilled all the way,,get a cut off wheel and take a little bit off the input shaft,,but MEASURE,,MEASURE and look at every detail before shortening the input shaft,,measure the depth of the crank pilot hole also,,