I have the 5spd manual in my 04, and the shifting is definitely not smooth. I find that it is most noticable from 1st to 2nd, and less so from 2nd to 3rd. I read of alot of people who experienced this same condition, and who also recommended swithing to Redline oil. I did and it made abosolutely no difference. I have questioned the dealer about this and they just say that it is just a "tight" tranny. It seems to me from feel that the flywheel could be heavier in the newer trucks and the pressure plate is to lightduty, therefore not grabbing quickly enough. It seems when I hesitate just abit longer before shifting after depressing the clutch pedal, the problem smooths out slightly better. I never experienced this in my 89' that I had. It didn't matter what rpm or how fast I shifted. It has not changed in 30,000 miles so I don't think its a breakin problem, just one of those design defects.
I have always wondered if switching to a heavier clutch like a Centerforce might remedy the problem.
Just my 2cents
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