Matt,
I'll put it this way....In terms of difficulty ONLY, the group consensus from most to least difficult was as follows:
1 - UNM South
1a - Paa-Ko Ridge
3 - Twin Warriors
4 - Sandia
5 - Black Mesa
Pacific gets the edge for two main reasons. I think that Pacific has the greatest set of par threes I have ever played. No two are routed in the same direction, they vary in length and required shot type, and the bunkering is more visually appealing. Plus, I had already seen so many drop shot par threes last week that it wore some of the luster off of 8 and 15 for me. That is not to take anything away from the par three holes at BM (4 & 11 were exceptional in my book, and 8 & 15 were very good) but you are asking me to nitpick. I also give Pacific the edge due its ability to induce the Boo Weekley pucker factor on tee shots. If your goal is to score at Pacific, you really have to tighten it up on 2,3,4,7,15,16, & 18. My thoughts on this could change upon repeat visits due my not playing the correct set of tees...See the answer to your third question for more detail.
For your third question, I had previously asked about which set of tees to play from at Black Mesa specifically. Everyone played from the blue tees with the exception of the 17 handicap who played from the white tees. Everyone had their best rounds (twice over with 36 holes) on Black Mesa. Conditions were nearly the same at all of the courses except for the last round at BM when a storm kicked the wind up to around 15-20 sustained. I now wish I had played at least one round from the back tees to experience the full effect of the tee shots at 7,9, and 10.