Well, I think the rules are more or less guidelines. Your goal should be to make a playable map.
Looking at a few items:
Territories that touch, but don't connect. - Generally a bad idea to have these.
Add some space between the territories, maybe put in a separate colored path to show some division.
An example would be the Men's and Women's Bathrooms at the right part of the top building. I see how it makes sense that it would only be connected to the lower 400 hallway, but many Warlighters would be confused that it doesn't connect to Harkola's office.
See the Japan Map for breaks in territories where there are rivers unable to be crossed.
Another thing that might need clarification is where rooms connect to hallways. Maybe make the hallway territories not end where there could be confusion, or you could add a door cutout to the Path that shows where the door would swing.
I realize you're still in testing/development, but it appears confusing when the lines go through other territories. Example: Mainly Sophomore Traffic has a purple line that appears to go to Special Ed Room, but I think what's happening is that the connection line is going through the building and over to Front Entrance.
Maybe you could clean this up a bit. Either re-route the line, or change how it looks. Consider stopping it short and putting an arrow on each end before it actually touches the territory. See Huruey's Castle as one example that uses the arrows and even dotted lines: http://warlight.net/SinglePlayer.aspx?PreviewMap=11704
Also, why do you sometimes have 2 purple lines connecting the same two territories? Consider making 1. EX: Video Column and Way to Canada.
Maybe you could have an outline around the elevator territory? Sorta like color coding. Why doesn't the elevator connect to Old Lower 400 Interior Hallway.
This caused the most confusion for me. I couldn't really get at what you were going for. Consider keeping the bonus links next to the bonus. Maybe the mega-bonuses can be separate.
Generally not a good idea to have single territory bonuses, especially of 4 value. They overweight themselves compared to much harder bonuses to hold onto. They may be a chokepoint, but still...
Clearing things up with school:
I wouldn't put anybody's name on it unless you had their individual permission to do so. Just put room numbers, or make a funny similar name.
Consider labeling upper/lower, etc. To provide orientation for the game players.