I think there is a bellhousing bolt going through a lower bracket as well. I had this same thing happen but it was a few years ago so memory is a bit hazy. I remember reading posts about this saying it was a major pia but i think the whole deal took 1/2 hr. I ended up bending the upper hold down bracket closer to the tube a bit then straightened it out when tube was in place. Been there ever since with no problems.
95 K2500 6 lug ecsb leather silverado, 2006 amg 18:1, kennedy exhaust, no cat, heath 2.0, heath boost control, ss diesel air filter, ata intercooler, high idle, bf goodrich 285/75/16 all terrains, remote pmd, three guage pillar pod