I knew you'd put some thought into it.
Why not wait and put new pads and rotors on together, that way you don't risk embedding the new pads with the crap that is on/in the rotors since you will not be resurfacing them they tend to act a little crappy for some time. (It may start another debate but the friction properties are not the same, and braking quality will be decreased).
When you install the rotors I'd suggest removing the pads and sand them down a little to remove the shiny finish they will develop over time. Sounds like more work but you are as ocd about brakes as I am so I would imagine that you would rather do a little more work since you should not have to be in there for another 40k or so.
