So to cut a long story short. I've got an 07 X with 59400 miles. And I've got two issues..
1. I have a vibration on the highway. depending on the day it could start at 45-60 mph, it's an excessive shake which I can feel in the seat and in the pedals. When I shift gears in the auto trans from drive to reverse to park and any combo you can come up with it makes a nice clunk noise. I've come to the conclusion that it has to be the rear u joint which has not been replaced. Am I correct?

2. I have a vibration in the steering wheel when I would attempt to slow down at highway speeds. I replaced my front rotors and pads and the vibration is still there. But this does not happen if I drive on back roads/town roads. Not a clue what this could be.

Oh and the X is still completely stock..

The first is most likely the ujoint like you mentioned. And I would have guessed the rotors would have been the cause for the 2nd. problem. But you changed them out. So not really sure what is could be.

Check your balljoints; mine caused some wheel vibrations during hard breaking. They were toast.

As for the clunk....
no idear. I had a manual transmission

check the lugnut torque, overtightened lugnuts warp rotors. factory spec is 85 ft/lbs or so

Interesting about the lug torque, never thought of that but makes sense. I'm gonna bring it in to get the tires balanced today and hopefully that's an easy fix for the front. I could have thrown a weight either on the great New England roads or the last run I went on. Hopefully they'll torque it down correctly.

As for a ball joint, I don't have the slightest clue what a bad/good one looks like. It will be going to Nissan to check the rear u joint and I'll have them check that out as well(I'm still under powertrain warranty).

Hopefully this is a quick/inexpensive fix! I'll let you guys know what happens. Thanks for the help!

make sure they run your truck for recalls because there is a recall out on the lower control arms. if your truck falls within the recall u get complete control arms, including ball joints

Thanks! I didnt even know that. How would a bad ball joint look? Would I be able to tell if I crawled under and looked?

Or I should say how is it supposed to look?

lift the truck by the lower control arm. grab the front wheel at the top and bottom then try to move the wheel by pushing on the top and pulling the bottom and vice versa repeatedly. a worn balljoint will allow excessive movement. be sure the movement is at the ball joint and not the wheel bearing. personally i havent seen balljoints cause vibrations so i would look elsewhere for the problem. u joints are the most common cause with these trucks

Road force balance...never heard of it until today. That's what the dealer said they did. There was one wheel they couldn't get to spec. They put it rear passenger to minimize vibrations if any from that tire. They even went as far as to pull the driveshaft out and check the rear u joint. As for the rear clunk they couldn't imitate it(of course not, never happens when you bring it in). We will find out on the drive home from work today if this fixed it. If so, I seriously underestimated wheel balancing...

And the service guy ran the X for open recalls, apparently mine doesn't fall under the open LCA recall.

So the clunk they are telling me is driveline slack. Happens over time as the miles get put on it. The driveline slack I'm aware of, I just wasnt sure it was supposed to be happening sometimes while driving. The conclusion is that my tires are cupped/uneven. And the rear tire that they couldn't get to spec is apparently wayy off. If I remember correctly he said it was off by 3-5kg? Not sure what that means, I also could have been hearing him wrong. Ultimately I'm very frustrated that my tires that have close 25,000 miles on them need to be replaced if I want the vibrations gone. I figured I would be able to get another year minimum out of them. Thanks for all the help everyone! I'm not fully convinced that tires are the whole issue. But we will find out when I eventually buy new ones.