Marvel Chronology Project

I am not sure if intended or overlooked, but on the forum pages, all the pages links normally at the bottom are no longer there.

It's because you're using the prosilver theme, which is currently the default.

Check this post for more background.

The A-Z links are on the main page, but some like Alternate Earths are missing. Is there a master list somewhere?

Links to every page are at the bottom of every page in the forum (as long as you're using the chronology theme) and running down the left hand side of every page outside the forum, except the home page. Go to any letter page and you'll see links to every page.