I have been tinkering around with a ton of settings, and seem to have everything back in line. Now WordPress is using my RapidWeaver theme (which required me to find a suitable RW theme 🙂 ), and it appears that posts and permalinks all look good again. Hopefully this is all of the mess I need to clean up today!
So I was playing with a spiffy RapidWeaver plugin to integrate WP into my RW site layout, and kaBlow! There went my theme. This is going to look pretty bad until I get this all figured out.