nonono, youre not understanding ??
the links in your footer — the theme author coded those with the assumption you would be using pretty permalinks.
Ive asked you about that first because IF you are intending to switch to pretty permalinks, then you will just end up changing those back, after having changed them here.
Your ugly permalinks.. have nothing to do with the footer. The footer is “pretty”.
Fixing the rest of them means switching to pretty permalinks which would in turn, fix your footer.
—
Back to footer:
I have not looked at your current theme’s files, however the following two lines ought to take care of the feed links regardless of what permalinks you are using (pretty OR ugly):
<a href="<?php bloginfo('rss2_url'); ?>">Entries (RSS)</a>
<a href="<?php bloginfo('comments_rss2_url'); ?>">Comments (RSS)</a>
Edit your theme’s footer.php or whatever file is responsible for that output.