I read the first page or two and the last page or two, so my idea has probably been mentioned already.
Have small give aways and or prizes for students going crazy or not. I would call it BIG BUCKS NO WHAMMYS.
During each segment of the game (segment = 4 minute interval between offical time outs) one of the in house cameras would focus on a random student - with no advance warning. Highlights of the student going crazy would be shown on the scoreboard. If he/she was really cheering hard, the fan is awarded BIG BUCKS or some other prize. If on the other hand, the student was not cheering then a big red 'X' would appear over the highlight of them on the scoreboard - the WHAMMY and they get no prize - and probably booed by the rest of the crowd.
This promo should be varied and run once each half. Sometimes at the first time out other times later in the half. It should not be predictable as to when this will be run. Hopefully, that encourages more students to cheer loudly and get into the game. In a couple games I would run the promo say three times, just so it is not predictable.
2nd idea. Since the students are suppose to sign in, the athletic department should know which groups are showing up in proportion to the number of tickets that group bought. So if a certain dorm floor or fraternity or sorority or campus club had a very good showing at the last game or games; have the athletic department/cyclone alley by that group a pizza dinner and have it delivered to them. Students love free and students love pizza. Combine the two and you have a winner.
Good luck and hope you are succesful in making Cyclone Alley better.