I never figured out a secure way of using mighty mounts with the kayak stacker (I have the old version - just a pair of vertical poles that clamped directly to the yakima crossbar), so I decided to get a load warrior. Since I'm only 5'7", its a nice place for my little stepladder. :p The load warrior has actually been useful on a few occasions - so if you do a lot of kayaking I would consider it.
I also mounted my old 48" crossbars just under the stock Xterra rack, using u-bolts dipped in that tool handle coating stuff. Worked great (and was cheap!), I now have the paddle rests to one side, and a Yakima viper bike rack on the other.
Good luck.