The wife and I went for a short drive from work to get some lunch tonight. Just before we got back to work, with no warning at all, the Bonnie just died. Engine, lights, cluster, power steering, you name it, no power to anything. As I'm pulling her off the road, I'm thinking battery died or something right?
No: the dome light, door chime, brake lights, flashers, power door locks all work fine.

-Try to crank her over, and nothing. Can't even hear the starter cranking. No lights come on when key is in ACC position either. Pretty much nothing on the electrical cluster shows anything, except the "security" light, which I have yet to t-shoot (i.e. when does it go on, and how long does it stay).
-Look at both fuse boxes for any smoking guns. Found none.
-Noticed a few strange things as the tow truck was on its way: Door lock buttons work, but nothing works on the key fob, not even the trunk release. Power windows and memory buttons don't work either. Security light was still the only thing on.

Recent major work in the last few years that could be related:
Aftermarket amp/subs installed, -wired by Car Stereo City
Intermediate shaft replaced (2X) -Dealership
Crank position sensor replaced (most recent) -Dealership

Don't have a lot of experience with elect. issues, nor do I have all the tools to t-shoot with, but...
Anyone have any suggestions as to how we can narrow this down?
Any help is greatly appreciated.

Well I feel like the world'* biggest moron. In a rush to get back into work I overlooked a simple variable. The 15A fuse in the under-seat box for "Ignition Switch" (duh). Yep fuse #29 was the culprit.
Pretty scary that one 15A fuse can take out that much. Especially when driving!

Glad you found the fix and it was just a fuse. I will make a mental note of this because something like this could cause a huge towing bill or other problems when we don't think to look at the obvious.

The more we work with our vehicles the more the tendency to over diagnose problems.