Figured it out!!
I was finally able to get the Map Book to work. I'm not sure what was causing the misalignment between the viewports and modelspace, but the fix was to edit the sheet template. I deleted the viewport, created a new one of identical size, reattached the placeholder, and saved the template. The next time I built the map book, it worked!
I now have a completed map book and sheet set. I've also discovered that AutoCAD has a maximum layout tab per dwg limit of 256, including the model tab. Yeesh. The remaining layouts are created, they just don't display as tabs along the bottom of the screen. They're still selectable from the map book or sheet set palettes, so at least I have a workaround.
In addition, I found a wonderful tool from JTBWorld that allows me to make mass edits (including sequential sheet numbering) to all my sheets/tabs/layouts at once. I'm pretty sure I'll be buying it tomorrow.
Thanks for your help. This has been a real ordeal, but I think I'm on the path to some form of increased productivity. The map book creator is a real lifesaver for larger sets, once you figure out how to bet it into submission.