The shaft end you speak of,, does the end that is flush on yours look the same as what should be sticking out? maybe the joint for the tilt mechanism is collapsed inside the column. IIRC when I replaced the lower bushing I had issues with the shaft end pushing up into the column. Did you try and pull the shaft out? If you post a picture to a free web host like Photobucket, Putfile or one of the thousand others, you can put the link on your post and then we can all see your dilemma.
89' YJ Larado 4.0L,AX15
05' Grand Cherokee Limited, 2"OME lift and a Hemi.