Lets start with the bugs. Most of these are just small things that annoyed me. While I doubt that most of these are bugs (judging by the state of the homepage and all the commented out code) I am just going to post these in here to make sure you know about them. Also, based on the fact that there are so many problems on the homepage I am guessing that it is a work in progress.
1) None of the RSS bugs on the homepage work. In fact, the rss feeds don't work at all.
2) Homepage doesn't show statistics. Judging by the fact that the statistics page says "Disabled for now", you probably already know about this.
3) The footers has plain text instead of links (and I am not even going to start on the fanfiction footer).
4) The advertising and site news sections of the homepage are blank.
5) Login/register in sidebar not linked (guessing because there is no login page for the fanfics but just letting you know).
6) It looks like you guys are rolling out the home page because the last 3 (news, shop and help) links on the sidebar (including help.portkey.org which is mentioned several other times on the page) will bring up the default apache page.
7) Fan art problems: not only does the updates box say "down for maintenance" but (as mentioned in the pinned topic) gallery.portkey.org brings up a blank page.
Now, about the search:
I know your Filter/Search page says that that it is in beta but I have to complain about it. The main problem is you can only do a title, subject or author search. There is absolutely no reason not to have a full text search. A few years ago I would understand why one wouldn't allow a full search (server size and server usage problems) but there is no excuse anymore. I often do full text searches right now through The Google using site:fanfiction.portkey.org but I can't do any sort of filtering of the results (for ships and such). So why don't you just scrap the search engine you have right now and switch to google?
I would also like to point out that it will even save you resources to do it this way. While I am not sure how you are handling the search right now and how your database is set up but all that you would have to do now is just set up the search params, do a get, take the results that google gives you and format it out to how you want it displayed. It could even be displayed in the current format you have. The only limitations is you need to put a 'search provided by Google' tag on the page and you can only get up to 1000 searches (and with about 5300 stories, this is a non-problem). And as someone who has just helped a small site implement a google based search engine, I can tell you that it isn't that hard and is much better then you could do on your own. I would even write you the code but I don't know how your database is set up and I probably don't know the language you are using (I am an application developer who knows enough about web development to get by).