Glad the swaybar link tip helped!
It does make sense that the boots would touch the lower control arms at certain arm angles under the right driving conditions. This is really a result of the fact that the spacers cause your suspension to operate in a "zone" that the components were really not designed for. Same thing with the knuckle/upper control arm hitting the spring. It's not an issue of the quality/design of the spacers or upper control arms (they're both good)...it's a limitation of the design of the suspension on the truck.
Stock explorers without spacers don't have either of these issues because the shock cannot ever extend far enough to put the suspension components in that "zone" where they start hitting/rubbing on other parts. By installing the 2.25" spacers, you are essentially making the shock able to extend 2.25" farther downward than it was supposed to be able to do. The BTF upper control arms really can't fix this...all they address/prevent is the stock type upper ball joints from coming apart under the accumulated stress.
Two things you can do to prevent the issues from happening. One would be to install a set of limit straps that let the front suspension only travel downward a limited amount before you have CV boots rubbing/springs getting hit. Unfortunately with the bigger spacers like yours, that doesn't allow for much downtravel at all before the limit straps stop it....doesn't allow for much suspension rebound going over big bumps. This is what a limit strap setup would look like:
http://www.explorerforum.com/forums/showthread.php?t=353043&highlight=limit+straps
The other thing (and really the better way to make this work long term) is to go with smaller spacers...I would suggest something like 1.5" front/1" rear. Should fix the CV issue. Yes, you'll still have the springs getting hit by the UCA/spindle as the suspension unloads, but the shocks will be able to extend further before it happens, so it's less likely. You can also install limit straps with the smaller spacers and lose less overall suspension downtravel than you would if you tried it with the spacers you currently have (this is what I did on my last truck).
Yes, the smaller spacers will make the truck sit lower...but that's what body lifts are for
