TinyPortal

So I tried making changes to QueryString.php to remove index.php from the URL for SEO purposes and this is basically what I did.

$scripturl = $boardurl . '/index.php';

Replaced with:

$scripturl = $boardurl . '/';

but that had an effect on topics as it seemed to break them everytime I clicked on a thread. Is there another this can be done?
I just want my homepage to be http://www.superheroalliance.net and NOT http://www.superheroalliance.net/index.php
That's about it. If it's contained in the link of topics I don't care. I just want my "homepage/main page" URL to NOT contain index.php.

Removing index.php from the URL has no effect on SEO just so you know. Search engines these days are smart enough to figure things out. There was a mod I think that did exactly what you did IIRC. If you need help with this I'd suggest posting at SMF since it seems to be an SMF problem and not a TP one. :)