Slight clunk when shifting in 1st

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I have a slight clunk when I shift into 1st (or any other gear) after coming to a complete stop. My vehicle is a 2004 dodge ram 1500 w/ a nv300 5 speed manual transmission and about 30k miles on it. I'm pretty sure it's not the U joint bearings since the mileage is so low, but I'm at a loss as to what is causing it.
 
It's to the floor when I shift into first. The clunk usually happens when I come to a stop and then shift into first or any other forward gear. I can make it go away if I shift very slow or very fast, I checked the the u-joint and bearings today and there was no play. I recently had the truck re-geared and had a detroit truetrac installed, could it have something to do w/ the rear end? I asked my mechanic when he changed the break in oil and he said everything looked fine and that a slight clunk is not unusual and not to worry (clearly I can't do that).
 
"After coming to a complete stop", or "When I come to a complete stop"?
Shift slow or fast at a complete stop? HUH?

I don't get what or when the problem is from these contradictory explanations.
 
Sorry I'll try to make it clear. It doesn't happen when I first start the truck and shift into gear. It only happens after I have been driving and then stop completely (rolling stop and it won't clunk when I put it in gear), as I'm shifting at a stop w/ the clutch pressed in it will clunk right as it goes into gear. I come to a stop in neutral and then shift into gear and that is when I hear the clunk. I can keep it from clunking a few ways which include rolling stop shift, really slow shift, or really fast shift (what I mean by fast and slow shifts is quickly or slowly moving the shifter from neutral to 1st).
 
We are back to clutch adjustment.
Even with hydraulic systems, you can adjust the total travel for a bit more, and adjust most of the free play out.
This will allow an earlier and more complete clutch dis engagement.
This should take only a few minutes.

Proper fluid is a must. This also may be a contributing factor. Since you are not experiencing problems dead cold, fresh premium transmission fluid is a good idea.
 
Alright I'll check into adjusting the clutch. The transmission fluid is pretty fresh, changed it about 5k miles ago but I will check the level. Thanks for your help.
 
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