So I assume you changed the harness that connects the individual injectors to the main engine harness.
If the two affected injectors were swapped around and work in the 1,3,4,6 positions, then your problem must be between the harness connector at the main injector harness and the PCM (Powertrain Control Module).
The other possibility is that the short caused a failure of the injector driver in the PCM.
I would first test the #2 & #5 injector with a Noid light, this is an LED tester that lights up when the PCM grounds the control circuit for the individual injectors.
This light should flash rapidly as the engine is running or simply cranking.
If it does not light there is a problem in the circuit either with the power supply or ground circuit.
In order to identify where the problem is you must check the individual resistance of the injector(s) circuit.
Disconnect PCM, Disconnect injector harness.
Measure resistance between each ground control circuit, if any or all show an open or short to ground the issue is in the main harness.
I believe all the injectors share a common power circuit, and since you are only getting 2 of the 6 injectors as faults the issue will likely be a shorted or open circuit in the main harness.
The other possibility is the short has caused the injector driver to fail in the PCM.
I would advise against installing a PCM until you have ruled out a wiring issue as the replacement PCM can be damaged as a result of excess current pulled thru the shorted wire.
Closely scrutinize every inch of the main engine harness between the two points listed above and I'll bet you will find a bare wire or burned/ overheated portion of the harness.
Remember the entire wire that shorts will turn into a heating element and burn not only its insulation off it will cut thru any wire in close proximity to it. You may have to cut away a good portion of the convolute tubing covering the harness to thoroughly inspect the wiring!
Good luck