[HO455]

You could having several issues contributing to your problem. Your rag joint may be completely worn out. The sliding joint that dmjlambert discusses, and the rubber in the isolation joint (circled in photo below) may have have failed. Or a combination of some or all of the above.

The second photo I harvested from the site as a comparison of how far the shaft should be sticking out.

The third photo is how I pushed my column up. My 67 doesn’t have the isolation joint. But doing it how I did it won't help with a collapsed rag joint.

Can you post a photo of the rag joint?

Notice the differences in how compressed your spring below the shift mechanism is?
You may have to wiggle the spring clamp around while pushing the shaft back up the column to recenter the lower bearing in the column.

Good luck and post your results.