shifter vibration t5 tranny

i got a 88 mustang gt with a bit of motorwork. i drag race it on the weekends and cruize it around town sometimes. recently i noticed a very intense vibration coming threw the shifter around 3500 rpms on up into the 6000s when i have to shift again it does it in all gears including neutral when i rev it. it does it with the clutch depressed and not depressed. it dosent matter if im sitting still or driving down the road. i took it to a transmission shop and they told me that it was my clutch. little did i know untill i replaced the clutch with the ford racing clutch that that was not the problem it still does it. anyone else had this problem and knows how to fix it. i know nothing about transmissions and little about cars what i do know i have learned on my own and from asking people please help.
 
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Check your trans/motor mounts. Bad motor mounts usually make trans mounts go bad as well.

+1. Motor mounts generally wear out before the tranny mounts do (oil exposure, etc) and the vibrations/etc will cause the tranny mounts to wear out too, especially if they're already old.

If you still have the plastic clutch fan, check the blade tips for signs of rubbing on the shroud. When the mounts wear out severely, the engine angle changes and will cause the blade tips to shear off against the shroud.