Ok fellas, just signed up. Alot of invaluable info. I have a 08 six speed. 2ND and 5 th cyncros had to be replaced with only 15,000 miles, covered under warranty. 4,000 miles later 2ND gear cyncros bad again. Get a call from service manager and he tells me that the short shifter is causing the problems "doesn't have time for the spinning to stop before entering second.they are going to replace the shifter.....what you guys think.

A "short shifter" doesn't change anything internally on the trans. It only shortens the distance your hand(and shift knob) moves during the shifts.It does allow for quicker shifts, for sure, but it also requires a little more muscle on your part to move the shifter, since the pivot point is changed on the short shifters.
My thought is it has nothing to do with the actual shifter, unless you just happen to hammer on it all the time.
Chances are there is too much clearance inside the trans, a fork is bent/out of alignment, or the previous "repair" did not get everything it needed replaced.

my 08 did that in the second gear shift till it warmed up. I shifted 1 to 3 when cold and after a couple of miles the 2 nd gear clash was gone