Holyshit, this worked! What I did was replace the "tuning" folder in 08 w/ the one in 07 and that resolved the substitution and fatique/stamina problem. Appearily the folder is repsonsible for sub ord and fatique, and possibly some other stuff. Now the players get sub as in 07, sub in when tired and player's stamina only slightly increase with timeout and end of quater. Overall the substitution is much better. However, we might run into the same situation in 07 where players who star the game are always sub in the last 2-3 min. of game, which is sometime I can sacrefice given how bad 08 is. I won't upload the files for those who don't have 07, as I'm not sure if it will be a problem with copyright. I'll let Andrew decide!
Also, CPU no longer waste time out just to sub in player. They sub players in during free throws and end of quaters!