I also have this vibration, ONLY in 5TH gear, so the clutch.pressure plate,t bearing, and the pilot can be eliminated as the drive shaft and related parts.
I have rebuilt hundreds of the std and world class (worked in Ford dealer many years, as a senior master ford tech) and for the life of me cannot visualize what the issue could be, I have read many posts on many different sites sending people on wild goose chases. (I'm sure not on purpose)
The only thing that I can think of (at this time) is the tail housing bushing and/ or yoke wear and overdrive puts enough torque to cause the vibration because ALL other gears are fine, if anyone else has a thought PLEASE chime in there may be several things i forgot --as i have been out of the bussiness for 10-15 years now (your mind forgets what is not habit)
Might be the 5th gear thrust bearing or something on the 5th gear shaft. Look here:
http://www.tremec.com/anexos/TRSM-T5-0510-R1_173.pdf
I've seen this develope after the dampener was removed from the rear end. Only once though.
The dampener was installed to add mass to the rear end and eliminate an objectionable howl that is particularly noticeable in 5th gear on some Mustangs with 8.8's. Not a vibration per se, but an acoustic annoyance nonetheless. My 2006 Mustang GT had it bad in 5th gear. Sounded like a bad ring and pinion. Ford issued a TSB on it since there were so many complaints.
I had an F150 once with a 4 spd overdrive manual that developed a vibration in 4th gear that felt exactly like tire balance, but it wasn't. Traced it down to a recently installed TRW U joint. Replaced the joint with a Spicer, rebalanced the driveshaft and it was smooth as glass.
Good luck. These type of issues can eat your lunch.