I had a similar problem years ago in my old 93 lx and it turned out to be my pilot bearing. Ended up doing a whole clutch while I was in there and the problem went away. It was bad I could feel it not just in the shifter but the car had the vibration as well. Once I replaced everything though it was good to go.
Adding to this old topic, noticed today my trans and whole car is shaking also it's only in 4th and 5th mostly from 68mph and up it's making a sound like a worn out wheel bearing would makes kind of a vibration and a hum, could this be a pilot bushing? Driveshaft seems fine, still have to change my fluid this weekend but just want to figure this out before it gets bad and more stuff wears out, also how hard is this to change and should I get the parts through tremec or is there another website that sells tremec components if this is the case it's 3550.