I'll speculate on the first-round matchups. I see that Pittsburgh did make it from USL-2, so for arguments, I'll move them into the "Midwest" regional. That leaves one more pro team to move to the Midwest; I have a funny feeling that it will be Rochester. (A second guess would be if they wanted to fly Miami up here.)
That would put a matchup of Michigan-Rochester. (Rochester could easily enough bus over to here, especially if they can shimmy through Ontario to cut the travel time.) Minnestota and St. Louis are the two "far midwest" teams, so let's pair them. That leaves Pittsburgh and Cleveland to match up with the two Chicago USASA teams, in some fashion.
And if you assume that Cleveland will beat their USASA squad, it would set up a good geographic pairing of CLE versus the MICH-ROCH winner.
Now let's quote the exact rules from the Handbook, knowing that rules are made to be tweaked, especially in the USSoccer world:
http://www.ussoccer-data.com/docfile/2008OpenCupHandbook.pdf "Teams competing in the First Round will be assigned to one of four geographic groups, each containing an equal number of professional and amateur teams. A blind draw will then be conducted within each group to determine all First Round pairings. The placement order of the First Round pairings will determine the match-ups for the Second Round. After the First Round, MLS teams will be added to the bracket for Third Round games based on geographic considerations."
"Pairings will be arranged to prevent the possibility of a lower division team playing a parent club (e.g.: Richmond Kickers Future [PDL] will not be pitted against Richmond Kickers [USL2], should both teams be in the competition in the same round) except for the Championship Game."
"Teams will enter the tournament and be matched with an opponent according to the following provisions:
-- First Round: Amateurs vs. Professionals. Eight USASA regional qualifiers and eight PDL squads are paired against eight USL Second Division clubs and eight USL First Division sides.
-- Second Round: First Round winners face each other.
-- Third Round: Eight MLS clubs enter to play eight winners from the Second Round."
(Having said that, I think that my pairings will be close to the actual. And I hope that the "blind draw" will be kinder to the Bucks than last year, which set up a matchup of the USL-2 and PDL champions.)