Jeff, did you ever get your subwoofer problem resolved? I have the same issue on an '07 Limited with the nav unit. The sub will work fine for a while, then cut out. It doesn't seem to be related to volume or any other stereo settings as far as I can tell, and simply switching the radio off and back on temporarily fixes the problem. Eventually the sub cuts out again. I don't think it's a thermal issue because clicking the stereo off and on resets the sub immediately.
I have a wiring diagram and a VOM but since the problem is so intermittent I'm not quite sure how to diagnose this, or whether I should try to have it professionally serviced at a dealership or an after-market stereo place. *sigh*