The interior squeaks and rattles have to be hunted down and fixed individually, unfortunately. But if you keep at it, you will eventually get them all. For more complete sound deadening, add a layer of closed cell foam, and then a layer of mass loaded vinyl on top of your Dynamat. Throwing down some dynamat and calling it done, just isn't the proper method. It will help, but to do the job right you need the foam and the vinyl. Most people won't do this because to fully sound dampen a vehicle the right way gets somewhat expensive. But it doesn't look like you mind spending money on the truck. Google sounddeadenershowdown, that guy pretty much has it figured out.
I'd check your wheel bearings, too. If you didn't replace them. And yeah the rag joint as someone mentioned. Also keep in mind that there is always the possibility that your steering box might need the adjustment screw tightened just a tad. I know you said the box is new, but you never know... could be things weren't done perfect wherever it was built/rebuilt. I really don't know how to tell when that adjustment is right where it needs to be, though.
But back to sound deadening, I'd get this for the doors:
http://cascadeaudio.com/car_noise_co...r_door_kit.htm