Thanks Evilhalfling! I think Greybar is the only one who still owes me this info, but I'll double check tonight.
Here's my proposal to fill the two open slots (LG & CE). I will pick the champion and two alternates based on some objective criteria (not considering the opponents). The last quarterfinal match will be LG vs. CE. The loser of the first quarterfinal match has the option to play one of the alignments. The player will pick an alignment and I will e-mail him my choices. The player can then plan the strategy, pick the equipment or buff spells, and flesh out the creatures for their announcement.
This process continues until we have two players for the last quarterfinal match. This way no player will end up having to fight himself.
For example, Greybar will be choosing the first quarterfinal match. If he chooses NG vs. NE and he loses, he can play either LG or CE since NG is out of the tournament.