Toyota Repair: Transmission 6 speed Cellica, cellica, shift forks

Question
Since I had a new clutch replaced in my 2001 Celica GTS I have had problems downshifting in second gear over 25mph. Down shifting at any speed above 25mph results in grinding the gear.  I took my car to the dealership and they now inform me that the car need a new transmission or a rebuild including 3rd gear,(which I now have a problem shifting into) syncro mash gear for 2nd. A total job of $2600.00 and all of this without opening the transmission before ordering the parts.  I also let them know the cluth is burning (which was replaced about 8000 miles ago).  My question is can the clutch if not installed correctly cause any of my transmission problems?  Milage on the Celica 125,000 miles.  Should a transmission be going out this early?  Ordering parts without looking into the transmission common?  Have you heard of any transmission problems with the 6 speed Celica GTS?

Thanks for your help and comments  

Answer
A grinding going into any gear or downshifting into a particular gear indicates a problem with sychronizer rings and shift forks and shift sleeves, these can wear and cause this problem, a clutch not working properly will cause a problem in all of the gears, especially first and reverse, there are no chronic transmission problems with this transmission.