1) I think Igor's suggestion of 5 player groups with 2 players moving on is too many. That means you are moving 40% of the players to round 2. If there were 8 players in each group then moving 2 on (25% makes sense). Too many players moving on is one of the reasons the tournament will drag on too long. If you are going with 8 groups of 5 players then only top player moves on leaving 8 players in round 2 and you can potentially finish entirely with 2 rounds. This speeds up the tourney by an entire round. Also remember that after round 1, eliminated players can go back to playing ladder games / fun games / FFA games /team games etc because most players are going to reduce the number of other games played when they have to take on 4+ additional games.
2) I suggest selecting 2 (maybe 3) default maps that *must* be used if players can't agree on a map. I'd suggest these be 100x maps (medium sized) but ultimately it's AngryOgre's tourney so he should make the final selection of the 2-3 maps.
3) I also suggest AngryOgre be the ultimate arbitrator of disputes in case where players can't agree on a map (then AngryOgre picks one of the default maps for them to play on). The same goes for handling complaints about a player deliberately stalling (taking max days to move over and over in a lost game) and be allowed to award a player a win in case where their opponent is stalling even if the game isn't complete.
4) I still believe 3 day turn limits is needed (mid way between 1 and 5). To speed up games I would suggest city capture % be set to 70% instead of 80. I'd also suggest NOT playing with ladder settings. The reason is that by allowing players to see their opponents city/army count you will definitely get players to resign faster knowing they are in a hopeless game. In ladder play many players probably play on much longer thinking their opponent isn't as strong as they are.
KGB