Inconsistent Permalinks work on some pages and not others

I am the webmaster for
http://phoenixhealingarts.net

I made a custom theme for my client about two years ago. It was my first WordPress theme. We recently upgraded to 3.4.2, and the website broke in a variety of ways. We did get it fixed: something about a file not needed in older WordPress implementations but now required — or possibly the opposite, my memory is not what it used to be. However, in the process, several things happened and the site is once again broken.

The site is hosted on GoDaddy. We changed from a Windows platform to Linux. We changed from shared hosting to grid hosting. Thinking that uploading the database backup might help, I imported the xml file I had saved, and we wound up with duplicate entries in the database. Some/most of these have now been removed, but there could still be some messy dangling duplicate entries in there. Here is the current situation.

My client called me because the H1 title and the image for that title had disappeared, and the site navigation on internal pages had also disappeared. Those are located in the sidebar in my theme. So I tried making sure the primary (containing the H1) and the secondary (containing the navigation) widget areas were active. That broke more stuff — so I switched back to both being empty in the widget area. I had also changed the custom menu, which also had duplicates.

I used /%category%/%postname% as the permalink structure. I have checked the mod-rewrite stuff when that is active, and it has the right content, namely:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

One of the pages was not showing up at all — (it went to the category.php file instead of page.php). I discovered that this page (health concerns) had mistakenly gotten subordinated to the services page. I undid that (moved it to toplevel/root of the website). This page then appeared, but other pages (which had been fine) now started giving 404-error results, namely: About, Egyptian phoenix, All of the services pages, and the contact page. The only pages that were still okay under the permalinks structure were home, resources, and the health concerns section.

Thinking maybe the problem was in my theme, I activated twenty-ten, and it had the same problem, permalinks were okay for home, resources, and the health concerns pages, and broken 404 for the about pages, services pages, and contact. This seemed like a really weird problem, so I called GoDaddy thinking they would know how to fix it. (Ha! Wrong!)

They advised me to switch back to the default (page number) in permalinks section — and then activate the pretty permalinks again (/%category%/%postname%). Using the default theme and default page number system, all the website pages show up okay. Returning to the permalinks, the same set of pages are 404-not-found broken.

So that my client will have a working website, I’ve had to activate the default twentyten theme with page numbers. (My theme relies on permalinks, and is completely broken using page numbers.)

I know it would be difficult to assess what’s wrong when the site is using twentyten theme and page numbers. However, all suggestions and thoughts are welcome. I’m desperate for help. Thanks!