I am not a ford tech but I am a gm tech and it works the same for us we can not just put a tranny or motor for thatmatter in with out tearing down and doing a cost analysis.It sucks being a tech in some cases cause we have our lift tied up for sometimes a few days.I can only imagine your frustration.I read a thread on svt performance about a guy who had a motor go bad in about 1000 miles and wound up having to go to court to get it setteld when it was a manufacturing defect cause the tech building the motor forgot to put a c-clip on the wrist pin.Appearantly ford is worse then gm in this manner either that or its the dealer.But it sounds to me being a tech that if the vibration is only in 6th gear it would almost have to be something in the tranny especiall if its getting worse after they tore it down it should be cut and dry for them to diagnose.I have rebuilt t5's but never a t56 but tomarrow I am going to pick up one of out firebird books and look at it abd see if I can see anything that might cause a problem in sixth gear.