Looking at possibly purchasing a 06 dodge 6spd 3500

As for the HVAC issues, grab a kit from Heater Treater. The problem with the blend door, recirc and other doors in the heater box is that they're hinges are plastic and become brittle after a short period and break. Most of the time it's due to the torque of the motor shattering the drive end of the hinges. The drive ears on the motor shaft can no longer engage the hinge and therefore, prevent the door from functioning properly.

I had my dad buy a full kit for his '06. It sounded like the blower motor was working harder than it should. We found that the recirc door had completely broken free, fell and was blocking inlet to the heater box from pulling air from inside the cab. It's certainly no 2 hour job. It'll take some time to pull the dash apart and prop up the lower half of it to give you access to the doors, motors, etc. It took most of the day to get everything put back together. We were taking our time and noting how things came apart since we were newbs to the task.
 
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About the blend door thing, I have 06 dodge myself and was wondering if blend door was my problem read a few things about it, it blows hot and cold air but it seem like it has a hard time doing it full blast and it comes out barely. During this winter if you cut the heat off of full blast your would freeze to death, air was coming in for the outside, felt like it was coming from under the front dash.
 
It might be a throwout bearing, but I'd bet it's the dual-mass flywheel. Either way, replace it with a solid setup while you're there.

Back windows are known to leak on these causing the rear underseat storage to fill with water at certain times. Blend door problems are to blame for the HVAC.

There are a few relevant recalls for this truck that you should check to see if they've been done. One regarding the steering linkage, one with fuel tank venting/filter, and one with reverse popping violently out of gear while backing down a hill.

They're good trucks overall.

So whats the fix to the back window leaking? And where does it leak in exactly?
 
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