Several notes:
First, that this is the best, most organized place you've found for information on the subject bodes not very well for the organization that's out there currently. We've got a great community that loves dominion, but as someone who's read every post here, there just hasn't been all that much on this subject.
Second, there should be some standardization as to the rules. There have been various tournaments I've seen, and various proposals, where you have: different ways of picking kingdoms, different numbers of players, wildly varying numbers of rounds, different ways of breaking ties, etc. And that's fine, I guess, but for something that are all qualifiers to the same thing, I would think you would want some uniformity on these fronts. We can discuss (and it's come up now and then) what the preferred options are on these things, but I don't know how much say you'd have on that anyway, and how much is up to Mr. Tummelson.
Third, Donald X., the game's designer, seems to be a great person to talk about the nuts and bolts of a Dominion tournament, if this is possible. And I'd guess it is - he's quite helpful when posting here. But you might want to have some specific questions to ask, too. Or not. I'm not sure, but I feel like he's the #1 person I'd want involved if I were looking at running a tournament.
Fourth, you need to have a strong set of rules, as regards to things like note-taking, collaboration, etc. etc. What constitutes it, how do you check for it, how much is allowed, what happens to people who get caught. We're probably a bit over-paranoid here, but hypothetical discussions about this stuff crop up. You need to be prepared for it as much as you can, and more importantly, you need to have a good set of people and procedures in place to deal with any problems, both the ones which are potentially foreseen, and any wacky things you might not have been able to guess at.
Fifth, you want to balance access and fairness as you can. I.e. geographically, you want to have a good number of places represented, so that I don't have to travel 1000 miles to get to a qualifier. The internet helps here. On the other hand, you can't just break it up geographically, because there are some parts of the country where you're going to get a LOT more players, and if you split on pure geography, you're making it much harder for people from those regions.
Finally (for now anyway), I don't know what your restrictions are here, either, but you want to have a balance as to the total number of seats, between letting lots of people have a chance, and having it be reasonably small enough that it's not a total crapshoot. I mean, I know Mr. Tummelson is more concerned with fun than with determining who the best player is. But even from a fun perspective, it's not so fun to get to only play one game, get a bad shuffle of the cards, and you're done. You want to have things be long enough that you feel like you had a real chance, or at least that if you didn't, it was epicly bad luck that you can reminisce and complain about for years to come
