I would inspect the water left behind after the Coral Rx dip. It is mostly clear and you can see if anything falls off - this will tell you what you are dealing with. I use a top-down port-hole viewer thingy so that I can shine some light underneath if I see something suspect. I don't do a bayer dip unless I get anything in the Coral Rx, but I completely understand if people do.
If you happen to knock off a acro crab, then save it and put it in one of your big colonies. They really are good housekeepers. I try and get them all out if I can.
I QT with the same lights that are in my display (HQI) - healthy SPS will quickly encrust the new plug which is a great sign... and if they don't then you need to watch them closer for pests. I would recommend that you light them like you want them to grow and look for them to respond as a sign that they are healthy. They will do better in the frag tank after this as well.
You forgot the most important piece - get SPS from people who know what they are doing. This won't guarantee no pests, but it is sure better than the reef herpies that go around at some frag swaps and shows. I also stay away from AQ stuff - if I really like one, maybe a frag later on after somebody else has messed with it but there is not to much AQ stuff that it original that you cannot get elsewhere. It should go like this:
0. Only get frags from trusted sources
1. Start your list