if you are buying an engine for this car and this problem I would wait until you know what the problem is. If your problem is with the power to the injectors a new engine won't make it run better. and if the problem is with the ecm not grounding the injectors still, the engine will not make it run better. You need to find the problem.
you have two fuses for the injectors. but they all have individual grounds through the computer. Can you unplug all four injectors on the bank that doesn't fire? Ohm out the four injectors. they should all be the same resistance, (11-14 ohms). If you have one or more that are a lot lower than the others that could be the problem. If they are all within spec, leave them unplugged and start the truck up. (It should run just like you said it does when all the spark plug
wires are off) while the engine is running check each injector harness connector for injector pulse. You can use a regular incandescent test light and see if the light flashes when you test both sides of the connector, using the test light to complete the circuit as if it were the injector. they should all blink in a regular pattern. If they all blink ok, plug them back on as the engine is running. Make sure you can do all this safely. with the engine running, each time to plug an injector back on the engine should run a little better. If that happens then that injector is working. if you get to one that doesn't make it run better that may be a bad injector. If that injector shuts down the whole bank that should be a shorted injector.
here's a video of a shorted injector that takes out all 6 cylinders on a V6.http://www.youtube.com/watch?v=41SZexc_ ... Y0wF2o5WUw
the low resistance takes the power away from all the other injectors. because your injectors have two different power sources that would be why only one side turns off. That's if you have battery voltage at both injector fuses. If you don't have power at both fuses check that problem FIRST.
just things to check. you should scan for codes to see what the computer sees and has recorded. Scanner would be the first thing I would use to figure out what is going on.