I'm guessing it came out cause the clip is missing.

 

That's weird. When I did my clutch I had to use a slide hammer to get my input shaft out and also to put it back in.

 

I just had the same thing happen to me just a few minutes ago. How did you get the whole thing out? The last boot keeps hitting the oil pump housing.

 

I am having similar issue....except on driver side, and I already did all of the above to get the Fing thing apart, new c-clip, and put in, only to find out that there is about a 1.5 inch gap between the cv boot and the side of the trans.....so logically thinking take apart and check everything, good, put together, no click, out comes the hammer, reassemble, and still a MOthafing gap.....except this time, i can't get the damn shaft out......8 pound slide hammer, slammed so hard it broke my pinky finger, still won't budge....anybody got a suggestion on how to get this thing out?