Since my last post I put a PA performance voltage regulator on the powermaster 200a alternator and fixed my voltage issue. I had 2 powermaster alternators come with cheap junk voltage regulators.
I had my stock T5 rebuilt before I dropped in the new engine but had an issue with second gear not disengaging the synchro fully and it burned up in less than 500 miles and started to grind again. I pulled it and the builder is taking care of it. Replacing the second gear set, synchro, slider, blocker ring. I am going to be selling this transmission.
I ordered the T5z from MDL for the 94/95 mustang and got the billet cluster support plate put in. I decided to go with the T5z for the 2.95 first gear and .63 overdrive to compliment my added power and 3.73s better. When I installed the new trans I am getting vibrations consistent with engine rpm similar to what i was dealing with earlier this summer. It feels like the input shaft is wobbling like its not seated in the pilot bearing. I combed through some old pictures and noticed my pilot bearing is pushed in too far in the crank and not flush. Then I checked the pilot bearing surface of the old T5 input shaft and it was noticeably wearing only on the tip of the input shaft. So I believe this is my issue and will be pulling the trans and swapping to the ford racing roller type pilot bearing.
Looking back on it I have been feeling vibration consistent with engine RPM since before I tuned it, and now that I swapped the trans out the vibrations feel the same as they did. I think the pilot bushing has been my vibration issue all this time.
When I installed the T5z I put in double adjustable control arms and set my pinion to parallel to the trans output shaft.
The top photo is my pilot bearing. The bottom photo is the better ford racing roller pilot bearing. A huge difference in how it sits in the crank.