MIL, Trac off, and check engine light and doesn't start on first crank.

Well, I just got back from college and i put the battery back in the supra and now when i try to crank the car, it starts up and then dies immediately, and the second time i crank it, it turns over fine and stays on. However, the MIL indicator lamp is constantly on, as well as the check engine and trac off light. Before i went off to college i didn't have any of these problems, and the car just sat while i was at college, so i really don't know what could be causing the problem. If it helps any, i installed an Apex-i S-AFC and a turbo timer before i went to college, and i got the same warning lights, but then they just kinda went away on their own.... So i dunno what to do. Any help would be appreciated. Thanks!