It was actually just a guessing game for the tuner. He didn't look at any maptraces or anything, he just decided to bump timing on certain parts of the map, I guess a psuedo smoothing factor. Took him all of 3 minutes to modify the entire timing map, and we just uploaded it into the car and took it for a spin.
I'm in the process of trying to better understand how the maptrace correlates to the actual fuel/timing map, so that I better understand what adjustments need to be made.
When you look at the maps in the BIN file for your ECU, they're really simple to understand. Just look at the Max TP column, at a given RPM, and there's your target timing value, and target AFR on the fuel map. Given you know what the targets are, you can do a WOT pull, see where your AFR's REALLY are, and then make adjustments to timing to acheive target AFR on the fuel map. You can obviously acheive the same results by adding or pulling fuel on the fuel map.
Hope I got this right, that's how I understand it, anyway.