Transmission/axle stub shaft insertion??

[Tiamat-red]

When I replaced my left front axle today the inner stub shaft came out with it. The part that the axle slides onto and the pin goes through. I noticed a groove on the inner end(the part in the transmission) that looked like some kind of clip should be there. I didn't give it much thought, being in a hurry to get the new axle in.
But now I wonder if this is a problem. Remembering that I had an extra shaft from the parts car when I replaced the right axle I looked and sure enough there is a clip on it. I checked the right side(which I replaced last week) and it is firmly secured into the tranny. So I put the clip on the left side stub shaft but I can't get it back into the tranny. Is this possible with the tranny in the car? I assume it is since I have the clip out of the parts car and that tranny is still intact. Should I try using my prescision adjustment hammer?
I jacked up the car to check the rear tranny mount.
This is when I noticed that the inner cv joint was about an inch and a half away from the tranny. And realized it should be secured.
But how do I get it in there???