I think I've finally decided on my conference alignment. Six BCS conferences consisting of twelve teams each (two divisions of six) with a conf. championship game, five non-BCS conferences with nine teams each where everyone plays everyone, and the three military schools as independents.
The only changes I made this time was to strip the Big East of their BCS status, change the Mountain West Conference to the Midwest Conference and elevate them to BCS status, and change the Big Ten to the Big North. I didn't add any user-created teams, although I'm still mulling over tossing in Montana and Appalachian State somewhere.
This is like the third version of this set-up...I really strived to not only keep teams together geographically, but also balance the BCS conferences. For example, the SEC was way too powerful in my first version, so I removed Georgia, Georgia Tech, Clemson, and South Carolina, and threw them into the ACC to improve that conference. So, if you see a team that you think doesn't really fit, the reason they are probably there is to balance out something. I've included the prestige ratings of each school, as well as the totals for each conference. Let me know what you think.
	
	
	
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		CONFERENCE RANKINGS
01  SEC
02  BIG XII
03  BIG NORTH
04  ACC
05  PAC-12
06  MIDWEST
07  BIG EAST
08  C-USA
09  MAC
10  WAC
11  SUN BELT
PAC-12
NORTH                     SOUTH
#  TEAM             *     #  TEAM            *
1  Oregon           6     1  USC             6
2  Boise St.        5     2  Stanford        4
3  Oregon St.       3     3  Cal             3
4  Washington       3     4  Fresno St.      2
5  Nevada           3     5  San Diego St.   2
6  Washington St.   1     6  UCLA            2
                   21                       19
---------------------------------------
WAC
#  TEAM             *
1  Hawai'i          2
2  UNLV             2
3  Wyoming          2
4  UTEP             2
5  San Jose St.     1
6  New Mexico       1
7  New Mexico St.   1
8  Idaho            1
9  Utah St.         1
                   13
---------------------------------------
MIDWEST CONFERENCE (MWC)
WESTERN                 EASTERN
#  TEAM           *     #  TEAM         *
1  Utah           4     1  Nebraska     5
2  BYU            4     2  Iowa         5
3  Arizona        3     3  Missouri     4
4  Arizona St.    3     4  Kansas St.   3
5  Colorado       2     5  Kansas       2
6  Colorado St.   2     6  Iowa St.     2
                 19                    21
---------------------------------------
BIG XII
NORTH                   SOUTH
#  TEAM           *     #  TEAM         *
1  Oklahoma       6     1  Texas        6
2  TCU            5     2  LSU          6
3  Oklahoma St.   4     3  Texas A&M    4
4  Arkansas       4     4  Texas Tech   3
5  Tulsa          3     5  Houston      3
6  SMU            3     6  Baylor       2
                 25                    24
---------------------------------------
SEC
EAST                    WEST
#  TEAM           *     #  TEAM              *
1  Florida        6     1  Alabama           6
2  Florida St.    5     2  Auburn            6
3  Miami          5     3  Tennessee         4
4  USF            3     4  Ole Miss          3
5  UCF            3     5  Mississippi St.   3
6  FIU            1     6  Vanderbilt        2
                 23                         24
---------------------------------------
SUN BELT CONFERENCE
#  TEAM             *
1  La. Tech         2
2  Rice             2
3  Southern Miss    2
4  UL Monroe        1
5  UL Lafayette     1
6  Tulane           1
7  North Texas      1
8  Memphis          1
9  Arkansas St.     1
                   12
---------------------------------------
C-USA
#  TEAM            *
1  ECU             3
2  NC State        3
3  Troy            2
4  Duke            2
5  Wake Forest     2
6  Mid Tenn St.    1
7  UAB             1
8  W. Kentucky     1
9  FAU             1
                  16
---------------------------------------
BIG NORTH
GREAT LAKES             GREAT PLAINS
#  TEAM            *     #  TEAM            *
1  Wisconsin       5     1  Ohio St.        6
2  Notre Dame      5     2  Penn St.        6
3  Michigan        5     3  West Virginia   4
4  Michigan St.    4     4  Cincinnati      3
5  Northwestern    3     5  Illinois        3
6  Minnesota       2     6  Purdue          3
                  24                       25
---------------------------------------
BIG EAST
#  TEAM         *
1  Syracuse     3
2  Pitt         3
3  Maryland     3
4  Buffalo      2
5  Marshall     2
6  Temple       2
7  Ohio         2
8  Akron        1
9  Kent St.     1
               19
---------------------------------------
ACC
COASTAL                   CENTRAL
#  TEAM             *     #  TEAM             *
1  Virginia Tech    5     1  Georgia          5
2  North Carolina   4     2  Georgia Tech     4
3  Boston College   3     3  Clemson          4
4  UConn            3     4  S. Carolina      4
5  Rutgers          3     5  Louisville       3
6  Virginia         3     6  Kentucky         3
                   21                        23
---------------------------------------
MAC
#  TEAM            *
1  C. Michigan     2
2  Bowling Green   2
3  Indiana         2
4  Ball St.        2
5  N. Illinois     2
6  Toledo          2
7  Miami (OH)      2
8  W. Michigan     1
9  E. Michigan     1
                  16
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INDEPENDENTS
#  TEAM        *
1  Air Force   3
2  Navy        3
3  Army        1