Yeah man you just have too much down travel and are binding CV's, happened to me too, even with OEM CV's. It made me mad that I couldn't run as much lift as other guys with equally equipped runner but it varies from vehicle to vehicle for some reason. One thing you could do is to take the spacers off the top or go to a shorter spacer, and preload the spring for more lift. This doesn't make the shock max length any longer so will give you lift without CV binding at full droop, the only downside is if you preload the crap out the spring it will ride terrible. I posted some info a while back about how the bilstein 5100's have a similar extended length to "extended travel" coilover setups from the big brands, so putting any spacer on top is a no-no, not sure what your shock measurements are though.
Your UCA's are definitely not the issue in this setup, look at how flat they are at static ride height. Maybe the boots were damaged during install?
See post #2 here for shock length discussion....
http://www.toyota-4runner.org/4th-gen-t4rs/223817-higher-angle-inner-cv-joint-options-4th-gens.html