I actually just dealt with this same problem - well, a problem I created when I attempted to pull the drivers side valve cover... when I removed and reinstalled the upper intake I severely damaged the rubber o-ring that goes around the portion of the EGR tube that goes up into the intake (it's a major PITA to get it to line up and go over smoothly - I'm sure the proper way is to actually disconnect the EGR tube, remove intake, then reinstall upper intake and reinstall EGR tube, but I was worried about damaging the EGR valve since the bolts are pretty well rusted and I didn't want the truck out of commission for a day while I got another one).
To get the upper intake off, disconnect the six nuts that hold it on, then you'll need to pop the back of the upper intake up off the studs (all six studs) then basically push the upper forward as you wiggle it to pull it off the tube. You shouldn't hurt the tube itself, it appears to be steel. You'll likely run into issues as I did on the reinstall, where you could damage the o-ring as I did... to make my life easier in the future I trimmed the elbow/curved portion of the tube off (you'll see what I mean when you get a good look at the whole tube). This makes removal and reinstallation easier. Hope this helps.