The Tremec conversions require cutting the entire trans tunnel out because they are so bulky. I'm betting this wasn't installed correctly and the trans is angled way down causing the u joints to be out of phase badly. One glance underneath should tell you all you need to know. Take a pic.
Oh and somebody labled that rocker for cylinder #5 with a center punch--no big deal just poor execution when a black Sharpie works the same.
J.Rob