Been a while, but here is my opinion.
1. Make the tournament 3 weeks long. 3 games in 5 days with weather issues is crazy anyway and isn't proper rest for a contact sport.
2. Let everyone in. Have a meeting for seeding purposes. Everyone is seeded. Bottom 20 would play on the first date, with top 22 teams (5a) having a bye. Adjust by classification. This would also allow teams from stacked regions to get in and make a run and the SCHSL would make a bunch of money on the extra games. Baseball and softball are still playing, why not soccer?
3. Have finals on 3 days. Thursday 2a, Friday 1a boys and 3a, Saturday 4a and 5a.
Friday would be 2, 4:30, 7
Saturday would be 10, 1, 4, 7
4. Separating them would be bad when you have 1 school with teams in both games. I'm sure the fans want to see both games as would some of the players.
5. This gives you some leeway in case there is bad weather.

That goes a little more in-depth, but I think would solve a number of different issues. Hard to have kids playing the biggest game of the year at almost midnight.