This is my first Dakota and when my research turns up nada I come here to ask.
I believe the main output shaft bearing is bad.
I'm hearing a metal on metal sound in every gear and that's the only time I hear it.

 

Can you hear it when the truck is not moving, in any gear?
Does it change as you apply/release the clutch?
Does the pitch change as you change gears?

 

Only in gear and when the truck is moving.

 

In all 5 gears, not sure about reverse and it stops when the clutch is applied or when in neutral at any speed. Doesn't seem to change pitch.

 

If the clutch is applied (released) then that would stop the input shaft from spinning. Going to neutral would isolate the countershaft. Very well could be the output shaft bearing.

First thing, have you checked the fluid level? What fluid is in the transmission? The NV3500 requires a special lube.

From the FSM: Required lubricant for the NV3500 is Mopart Manual Transmission Lubricant, P/N 4874464. This is the only lubricant to be used in NV3500 transmissions.
No other lubricants are acceptable, or recommended.

Can you post a clip with the sound???

 

If it's four wheel, it might be the transfer case.

 

The fluid isn't low, so chances are it is the output shaft bearing. I also noticed that the rear drive shaft gets quite hot.