I finally got the control board back in and did a another test spin on the jacks. It was great for 5 minutes, and then the stupid ticking came back. AAHHHHH!!
I called it quits for the day and went back to my school work. This weekend I will take everything apart again (I will have this motor decoupling down to an art soon) and on Monday try to get the holes on the motor plate countersunk. The torque converter bolts and one of the motor bolts is a heck of a lot closer than I originally thought, so even with a slight pressure the bolts hit each other.
I may try a test drive up and down the drive way again and record it to have something to post, and to show off the annoying ticking sound. That and I want to test out the drive train to make sure it actually works and hope I don't have to solve more problems.