Nathan, some of my thoughts: unless the room is square or nearly so, the best location for the sub is generally the corner behind the speakers, so I'd suggest using that location at least initially.
When you first tried the calibration the sub's level control was so high that the 2600 couldn't reduce it and increase the speakers enough to get a balance, so it gave you the W3. Lowering it to about 40% made it, but just barely(the +10dB used up all the adjustment), so I'd suggest to allow a little more adjustment room that you run the calibration again with maybe a 25-30% setting on the sub level so that all the numbers will be a bit closer to 0 after the calibration. For the calibration, set the 2600 to "skip" for speaker size and manually set all speakers "small" with an 80Hz crossover. I'd suggest that you try the "natural" setting for equalization initially(or you could "skip" equalization at first and leave it for later experimentation)which gives more emphasis to equalizing low frequencies and less to highs. This is similar to the equalization setting on the 2400 which I helped a colleague set up which emphasized the lower frequencies and gave us a pleasing result. As always, when you have the time, experiment with various settings.
