99 GT New Engine But wont Turn over HELP PLZ

[RobGleich07]

I have a 99 Mustang GT, When i bought the car it had a 5.1L Stroker from a 4.6L with a Procharger. Well it through a rod the day after i got it. Now i have the complete engine rebuilt. The engine is in the car witha new transmission. Well i belevie ive got everthing hooked up. The Car will not turn over when i turn the switch. However when I by pass it by the starter it would crank for a couple seconds then cut back off. I thought it was sumthing withe the Anti Theft system or sumthing but i need help. Im a college student with no car and no way back home and forth to school. Also you can take a look at the car at http://www.mymustangsite.com/KandyMustanGT/
Thanks Rob