We did a complete rebuild to the top end of my motor, but we forgot to label the injector wires. We plugged them all back in in the way they wanted to lay, but if we mixed a few of them up would there be any consequences besides a bad misfire?

TPI's are batch fire injection, they fire one side of injectors at a time. So you woundnt have a misfire. from mixing up injector plugs on the same side of the engine.