When did you have the carrier unit lowered or adjusted. The housing isn't supposed to be adjustable. It shoud be mounted to the frame. I suspect you have a funky u-joint and changing that angle just took away the sound, but not the problem.

 

It is mounted to the frame but has several different mounting holes.

It seems much better now. I'm also going to change the leveling valve, I noticed my ride height seems to vary too much.

All of the yokes are in phase as well, thanks for the tip.

 

I bought one of those magnetic angle thingys, but am confused on how to use it.

How do you calculate yoke angles where the other side of the yoke goes into the tranny or the diffs? It's impossible, as there's no flat surface on the yoke.

The way I understand it is this:

You want the tranny yoke to be level, with the first driveshaft level to the hanger bearing. From there it should go down slightly to the front yoke on the front diff. That d/s is measuring 2 degrees UP to the first yoke. Then the rear d/s should be 13 degrees, both yokes pointing slightly "up" in comparison to the d/s.

 

I'm not sure about that. My 9400 has a solid set between the trans and the carrier bearing, then after the CB the shaft dips at a shallow angle to the frint diff, then the front to rear diff line up at a steeper angle.
I would check with your dealer.