The AIS operates under various predetermined conditions. Most common condition is when the throttle is snapped shut, which wouldn't necessarily affect dyno A/F readings, but the AIS valve can open for other reasons. For example it is fixed open until the engine is fully warmed up.
The biggest problem with the AIS enabled on a dyno is you (the operator and the dyno machine) don't know what it's doing. In order to have an effective dyno session and build a good map the AIS needs to be taken out of the equation. Seastar are reputable dyno tuners, so I'm a little surprised they didn't clamp the AIS pipe before the first run?
To block the AIS read this thread:
http://www.xt660.com/showthread.php?t=5544
As for the power/torque it varies from bike to bike and different dynos read differently. Really you should only take not of your figures for tuning purposes and for comparing different mods on your bike. However, as I said earlier, your torque looks good, if a little lower in the rev range than I would have expected. A stocker makes 56Nm(41 ft-lb)@5500rpm, so yours making 46 ft-lb is an improvement, but it did peak at 4700-4800rpm.
Something's not right though. 17.5:1 is extraordinarily high. Besides blocking the AIS are there any air/vacuum leaks? One thing that does give ridiculously high A/F ratios is a perished throttle body to cylinder head intake hose. It's not unheard of for them to go porous even on relatively new XTs. Modern fuels containing ethanol give rubber parts in the fuel system a hard time. What's it look like? Any cracks? Any bubbling?
It might be a good idea to join the Supporter's scheme for a tenner and then you can post a query in the Ask Kev section. He's put more XTs on a dyno than anyone and will be sure to have more ideas/suggestions than I can offer. The link to join is in my signature line.