Transmission Vibration??

I have a 94 cobra with 3.73 and stock driveshaft. I have a nasty vibration through the shifter and i can some vibration through the pedals. Vibration is there with clutch in or out and transmission in neutral or in gear. Vibration comes more noticeable with rpm.
Tires have been balanced and the front end has been aligned. I have not had the driveshaft balanced yet. Transmission was rebuilt 5 thousand miles ago, replaced clutch and resurfaced flywheel. I read on on thread that it should be the front bearing of the transmission if it causes a vibration when it is in neutral.

I pulled the transmission already i am going to replace the pilot bearing, clutch and throw out bearing, and transmission mount. I do not know if i should take my tranny to a shop to have them look at it or not.

Figured that it should not be the bearings since they are only 5k old.
Any ideas???

Balancer is good, will a tranny shop be albe to tell if it is bent with out tearing it down?

The vibrations increase with speed also. I do not like to go over 70 vibs are to bad. Over 1500 rpm the vibs start to get bad and if i put in clutch still there, and also if i put it in neutral still there.
Thanks for the replies, i guess i will get the DS balanced and hope this helps.