Matt, tell me about it. I just put A/C in my truck, didn't come with it from the factory. I took my old box out and replaced it with a unit from a donor truck. So in essence I did everything twice(I took the box out of the donor truck myself), double not fun! That definitely makes sense to cap off the heater core lines to improve A/C efficiency.
Believe it or not it's nicer out in AZ than it is here some days. I'd gladly take 115 degrees and 0% humidity over 95 and tropical type humidity. I'm so glad A/C takes out the humidity.