When I'm in a higher gear, 4th/5th/6th, ther is this whining/whistling noise coming from what seems the rear of my car. But if I press in the clutch and take it out of gear (while still driving), the noise goes away. As soon as I put it back in gear, the noise comes back. Also, when I'm in 6th gear at about 50mph (I have 4.10's), there is a chattering noise that will go away when I push the clutch in and take it out of gear.

What could this be?
It shifts fine, stays in all gears, and drives perfect, other than the noises.

 

Sounds like the whining could be the rear end. I don't know a lot about setting them up but I know there's a fine line between adjusting the pinion and it can exhibit whinning when accelerating, coasting, or decelerating based on how it's installed.

 

I vote for your 4.10 mod as the cause.

 

I hope so, I don't have funds to rebuild the trans! I'm actually getting rid of the 4.10s for 3.42's so maybe that will help.