6 sp. Manual Woes

Hello all, I recently purchased a 05 doublecab TRD with the 6 speed
manual with 55,000 miles. I have 2 transmission/driveline related questions.

1) While coming to a stop I can feel a bit of a clunk every once in a while just before coming to a stop or when rounding a corner. I can't really tell if this is in the tranny or the driveline somewhere. This seems to happen whether the truck is in gear or not or whether the clutch is in or not.

2) When shifting between 2nd and 3rd gear there will sometimes be a small clunk feeling in the transmission, almost like the syncromeshing between 2nd and 3rd is slower than all the other gears.

I have read of the driveline clunk before but noticed that is mainly
only people with the automatics that are having that problem.

This vehicle was bought certified used and has the extended powertrain
warranty. However after purchasing the vehicle I found out the
transmission in the truck was replaced by the dealer only a few months
before my purchase. Also I have tried to get the TSB springs but the
dealer will not do it because the truck has 55,000 miles.

Thanks for any help you all can provide.

 

I've felt the clunk before on my '05. It happens so rarely, though for me that I just didn't bother looking into it.
While in 4wd the tranny is a bit harder to get into 3rd than the other gears.