Hum kind of looks like the Pilot Busing is Cocked a little at an angle in the second Picture above but that maybe from the Camera Angle, otherwise the Bushing looks to be installed all the way in and Flush with the other Edge of the Crankshaft Flange just like it should be. And you can sure see were the Input Shaft was hitting the Pilot Busing hard, this is looking like either your input shaft is too long or "drag-200stang" might be onto something with a Thrust Bearing in wrong position, something sure is moving things in the wrong direction for things to fit properly.