Hi Evan, to tell you the truth, it's very hard for me to 'completely' help you without “seeing” what you are talking about =P. So, if you could, please either PM me the link or post it publicly here…
At any rate, I think you may be having a problem with the 'activated' Math Comment Spam plugin. Basically, if you go to single post and look at the comment area, you “may” see the FUNCTION not Defined error threw up by the activated plugin. So, what happens is, often if there is a “FUNCTION Doesn't Exist” error, the site/widgets does not display properly.
Evan: “Another problem is that the Links widget won't move out of the sidebar.
Even though I have moved it out, the blog still shows the Links section
in the sidebar.”
M.T.: It's may be because of your Browser Cache (you'll need to clear cache =).
Again, I'll need to 'see' what you're talking about to be able to help you.
Evan:In “Presentation,” the 'Menu” option only appears to allow the pages to be shown in the Header menu.
M.T.: That is the only place it's coded to have the menu. To place the menu pages any where else, search on Google/WordPress codex for “wp list pages” php function. To give you an example, you'll just place < ?php wp_list_pages(); ?> in one of the Samsarin PHP widgets to display the WordPress Pages.
Best regards,
~Mint Tree~