Archives & Comments not working

I don’t know if I “over-formatted” (I admit, I deleted huge chunks of the main-index template), but clicking on comments or archive links sends you… well, the pages aren’t generating, I suppose.
I’m not really familiar with PHP and I’m very picky about not wanting to stay “default” concerning my templates… My website (weblog) is at http://www.mell-o.org/ and my index (where my posts go) is at http://www.mell-o.org/wp/index.php/ . My question might be “newbie”, but I’m very unsure. How can I get comments to work, as well as the search field in the archive search/archives?
=(