You have to modify quite a bit for the engine to not want to run with base engine settings.
If all you did was body work, and the engine was running fine before, you have to just stand back and start with the basics. Check all cables that come from the battery. Make sure they are tight at their connections. Then check the alternator connections. Check the spark plug wires. Disconnect and reconnect each wire at the spark plug to make sure it has good connection. Do the same at the coil pack. Check the harness connector at the coil pack. Check the Harness connectors at the DIS. Check the connector at the CAM sensor, and the connector that goes along the water pump down to the crank sensor.
Get the motor so that the starter can crank it over good and easy. Then if the motor starts, but stumbles, play with the throttle while it is stumbling. If the motor turns over good, it will fire but stumble.. then check battery voltage while it is stumbling. If the alternator isn't working and doesn't bring voltage up around 12v, the ignition system may be struggling.
Also start checking the fuel pressure when it's struggling, and when cranking. Make sure you're seeing good pressure at the rail that isn't fluctuating.
Then finally you may want to pull the plugs and take a look. They could be fouled from all the attempts you have had and need to be dried out (if they are double platinum) or replaced (if copper).