When you change the injector, the cylinder fills with oil, and fuel. You did pull the glow plug and bar the motor over after replacing the injector to clear the cylinder, correct.
The High Pressure Oil System is now full of air. Before the truck will start, the starter must crank the motor over enough to build and refill the system. It does not get all the air out, but it will start. Running the truck and doing repetitive hard starts will clear the system.
If you made the batteries clear the cylinder, you just put a lot of crud in you exhaust system, including the turbo. And you made the starter work very hard (ever heard of hydrolock) to first compress all that liquid and than shove it out a small exhaust port.
Charge the batteries and hope you didn't bend a rod.
P.S. Do not turn the motor over for more than 20 seconds and let it rest for at least a minute between tries.