Just to say that is a really cool bit of design work there, I'm very impressed at how you've got it all lined up. Yes, the extra space at the bottom is because you've used
position:relative; with big negative values to pull the letters up the page.
A quick play around in Dragonfly suggests that you can set a height on
#content and it will crop the content div at that point but will leave the relatively positioned text exactly where you want it. You can set
height:1em; if that's all you're having on the page, or work out the relevant height in ems (which should be pretty consistent across browsers, if you're lucky) if you need anything following the crossword.
Disclaimer: I have tested this in Opera 11.5 but nothing else!