It seems that in Yak's "Fix things that should be fixed, but they really don't need to be fixed now because there's more important stuff to do" spree, the usericon on the front page news items has been made significantly larger. This, of course, has added more empty space to the page, joining the rest of the empty spaces in the header.
The code is a mess, and fixing the "important stuff" is massively unrewarding work, however necessary it may be. The work involved is probably highly tedious. You'd probably have to replace code that takes user input with something less fucktarded, but here's the catch- in a well designed code base there'd be a couple of classes that dealt with actually issuing SQL, reading and parsing user input, etc. I.e. that sort of dangerous stuff would be limited to a small area, and more importantly it would
exist in only one area. You would then make good use of inheritance to build layers on top of that. So when your DB code needs fixed, it can be fixed in one place, end of story.
But it's likely that there are mysql_query() calls and echo() calls littered throughout the code, and I'm sure the pattern (hah) in which they are used is inconsistent, so you can't just do some semi-robotic find and replace type operation. You'd have to decipher each part of the code, figure out what it does (and what unintended behaviors other parts of the code may be relying on) and then rewrite it in a secure way. All of this is extremely fragile, because without any sort of modularization or information hiding, you have no idea how your changes will affect other parts of the site.
Frankly, if these were any kind of reasonable adults we were dealing with, any hypothetical "consultant" would likely tell them to throw the code base out and start over anew. Which is a whole 'nother can of worms as we all know.
Yak probably lacks the motivation and skills to do anything like this. It's also more immediately rewarding to do stuff like play with CSS templates, especially if you're lazy and unwilling to wait for hard(er) work to pay off.