Noise & Vibration out of T5 in low speed/high torque situations

Another thing I ran into after doing the T5 swap in mine was the little inspection plate wasn't fully tightened and that gave me an awful little metal on metal noise that freaked me out the first time I heard it on the maiden voyage. Definitely had me a little worried seeing how over the winter I had fully rebuilt the T5 tranny for the swap that had a shady past (kid shipped it to me before i even paid for it, so I was surprised it wasnt destroyed) and put in the 3.73s. So all noises were causes of concern but they turned out to be the tranny hitting liek we discussed, the inspection plate and then my O/R H pipe was making contact. After that, noise free.
 
Ok I dont know if this will help you but mine was making almost the same noise you are describing but in 5th gear at 75-80+ and the faster you got the worse it was and you could feel it through the shifter, well I tore my tranny down last night and found that a peice of my broken shift for and one of the plastic tabs were lodged in between some teeth on 5th gear. Hopes this helps