A quick question. Can the two wires going to the fuel injector cause a misfire if they are bare and touching each other?

 

Yes.

All the fuel injectors get 12volts when key is on, should be one Red wire that daisy chains from one injector to the next, thats the 12volt wire.

Then each injector will have a separate GROUND wire that runs back to the computer, so in a V6 there would be 6 different colored wires as the Grounds.

A fuel injector, electrically, is just a coil of wire around a metal core, when an injector is Grounded by the computer that coil becomes an electro-magnet and pulls open the needle valve which lets fuel flow into the intake.
Ford uses 11-18ohm coils in the injectors

A short between the two wires is 0 ohms
Electricity ALWAYS travels on the easiest pathway
So "its" choice of pathways is 0 ohms or 11ohms
0 ohms will get the Ground, injector will not so won't open and let gasoline flow

 

Thanks