First off, I really like the judging system. I tend to go over the nominees of each category and see whether something interests me - and there are products I've never heard of or that I would have never considered buying otherwise. And then in the end, the fans decide.
I would *not* want a write-in option, in fact, I am really biased against such an option. In my mind, it would either be worthless (for unknown products) or would lead to popularity and not quality winning the prize. Bigger publishers have a *huge* fanbase, and if they all wrote in a product like, "Legacy of Dragons" (a book that I love) just because they might not know the other, smaller books, I don't think that's fair any more. Now, I'm not saying LOD wouldn't have deserved the prize; I consciously chose an excellent book, albeit one with a large fan base.
And perhaps people would even write in Draconomicon, and that would win the prize despite WotC not even entering the book?
No, please no write- ins.
I think a judging period of one week is enough, but you must declare the judging period at least a month before. That way, publishers and game sites can advertise the date in advance. Just like elections, you just have to know up front when to vote. If you just put the booth up when it's ready, you should include a longer voting period or guarantee at least a certain time frame where it's open.
Also, the voting booth should be accessible (or at least linked to) via the official GenCon site (I don't know if it was this year).
ETA: Re: Financing. You might want to make a special badge/prize/something that you auction off at the show. What I mean is an American Auction (I think that'S what we call it) where you let a hat go round, and the last person to put in 5 dollars gets the prize. 5 bucks is not that much, and it tends t go really well. It'll probably not cover all the costs, but it'll help.