Not meaning to ask a stupid question, but I've been down this road before with a Nissan and a Mazda dealership being COMPLETELY unaware of a TSB until I printed it out and put it in their faces.
Is your dealership aware of the TSB Ford issued to fix out-of-balance clutch assemblies? That sounds to me like it's the problem you have if your transmission is shaking the car.
Bulletin Number: CSP-11B31
Sequence Number: 10043326
Component Name: 101000 POWER TRAIN:CLUTCH ASSEMBLY
FORD: SEE DOCUMENT SEARCH BUTTON FOR OWNER LETTER. CERTAIN MODEL YEAR VEHICLES HAVE AN IMPROPERLY BALANCED CLUTCH ASSEMBLY. THIS WILL CAUSE A VIBRATION FELT THROUGH THE SEAT AND/OR STEERING WILL WHILE IN PARK, FIRST GEAR AND NEUTRAL