where am I going wrong?

My CFII seemed to have a very fat disc, that allowed the fork to move very far forward towards the rad. So I used the short rod. I'm pretty sure the OEM rod was longer than 5.5
The release forks need to be matched to the pivot tower.And the tower centers the fork in the window vertically and towards the front, so that during clutch disengagement there is someplace to go. So if yours is so centered and properly installed under the TO clips, then tho only other difference is the outside length. And if that is wrong for your Z-bar, it won't even work.
If I had to guess at something, I might choose a too-thin disc, or an engine mount not installed correctly.
Make sure the Zbar is sitting very near to parallel to the ground and at 90* to the vehicle centerline as viewed from above.The pedal downrod should be well centered in it's oval opening, and all the nylon bushings installed and the clip installed that keeps the bar from traveling sideways.