Mike,
I did get the problem resolved. I had been using a plugin called "Custom Post Type Permalinks" which had been working for me until the upgrade. I removed the plugin and reinstalled it (even though it has not been tested with the current version of WP). Once activated, I went to Settings=>Permalinks and edited the default settings for custom post type permalinks. I also discovered that after the WP upgrade the category settings for custom posts had been stripped. Specifically, the checkbox for the parent category had been toggled off, leaving only the child category selected. This resulted in 404 errors for custom posts because the permalinks didn't match the slugs. To remedy this, I had to reselect the parent category for each child post in the post editor.
Hope this helps!