Ok i have found the problem after I got the box out of the car, I noticed the gear the steering column actually attaches to, all the teeth on it were pretty badly corroded. So I put it all back together and tested my theory and i am correct. The "CLUNK" sound I am hearing is it skipping 2 teeth and then catching the bolt.
Pic for reference.
So outside of getting a new steering box and possibly that joint it's pretty screwed. My temporary solution is to weld the gear directly to the joint. Any better ideas???