Unfortunately by default MySQL searches only on words with four or more letters.
This can be changed by setting the variable 'ft_min_word_len', but this is not a dynamic setting that I am able to change. I would have to have access to the MySQL config file, and then restart the web server (and rebuild the database indexes) for the change to take effect... I don't think that's something that is going to happen unfortunately.
This is pretty standard tbh.
I had intended to give the search page a bit of love, because as you mention it's pretty nuts'n'bolts right now. Will see what I can do to clean it up.
Edit: starting to improve the formatting, plus a few things under the hood. I don't think the search is too bad really
http://opal.lunarbreeze.com/~snark3/index.php?p=search&query=search%20formatting&sec=forumsp