tranny vibration

Check your trans mount, I know mine was loose at one point when I checked it after I noticed some vibration. Tighten the sh1t out of it. Could also be a motor mount too.
 
Shifter is the first thing to check, but did use replace the throw out bearing? I would think you did, but I thought I'd ask. Did you get your flywheel turned also?? Another thing to check is if the bell housing still had the dowel pins in it. If those were missing the bellhousing could be mis aligned.