Well the shaker amp has been draining the battery, so it ruined it somehow, although it could have just been old (Not sure, just bought the car a month ago). After i bought a new battery it was working fine until this week. So, I left it un hooked for a night so it wouldn't drain, and when i reconnected it to start it it started up fine. I removed the fuse to the radio, not the amp after i shut it off, and when i tried to start it later that day i could only crank it a few times, and when it did start it just shut off after a few seconds.
The tuner i used was the SF3 from AM, and i reflashed my 87 economy tune, didnt work, so then i flashed it back to stock and it still didn't work.
Oops, i that was by complete accident! Obviously i meant to post in GT tech. Although this could apply to a v6 as well...but If a mod could please move it to the correct forum that would help me out a bit...

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First car, 2006 Mustang GT (See avatar) Bought on January 17, 2009
Mods: SCT Tuner, SLP Loudmouths, JLT CAI, Steeda sport lowering springs, BMR adjustable lower A arms, Roush hood scoop.