Hi there! Back on this issue for those who'd want to use these two great extensions, AGS and sh404SEF:
Actually, using the J! router for the "com_content" in sh404SEF kills more or less the whole thing, because you bypass all the sh404 settings you intended to change the J! normal treatment and, even using the "modern" SEF setting in J! (to get rid of IDs in the URL) won't do it.
But one line in your response caught my eye: "Are you using a filter module on articles page (com_content)?"
Since AGS is a module, I can put it anywhere I want, not just on a "com_content-generated" page. So this is what I did:
1. I created a "Search" tag in the Joomla! tag component. I called it "Search" just to remember what it is, but you can call anything.
2. I created a menu link to a page pointing to "Tags > Tagged items", and assigned my AGS module to it
3. In sh404SEF configuration, in the "by extension" tab, I put "Use Joomla! router" and "Use Joomla! router.php" for the Tags extension, instead of the "use default handler" ans "use sh404 plugin if available"
4. After saving that config, now the pagination on search results works as expected on my search page, and my articles URLs are still the way I set them up.
1. To have a cleaner result, I got rid of the tag component output at the bellow the search results. There is one because, although the tags are not used in this site, you still have a minimum of output displayed. You can get rid of the search box, the pagination, ... in the tag extensions options, but you'll still have "something" displayed.
What you do to get rid of this will depend greatly on the template system you use and/or your understanding of Joomla! override. In this case, as it was a Warp7 template (from Yootheme), it was easy: I created a new "layout" in the template where I can choose to hide the "system output" (that's the terminology to designate the content generated by the component on the page), and assigned this layout to menu item I created in #2 above. That way, on that page, I have only the modules output, not the component, so no trace of the "Tags" output.
2. I chose "Tags" because there are not used on that site. If you do use them, this *may* affect some of your URLS. I assume I can achieve the same result using the "News feed" component instead (I've build J! site for 13 years and never used it once).
So in any case, all is working fine now. It's a great way to search articles when you use custom fields.