[RICK LAKE]

Sambo You are over thinking the problem Start #2 and 4 are dead
Pul;l valve cover and make sure the rockers are working to those holes
compression test next looking for min of 150 after 4 complete cycles
If compression is good go with fixing 1 cylinder at a time
Get new spark plugs for 2 and 4. See if you have a miss Test at idle and at 1,500 rpm.
Next swap injectors with good ones from other holes If missfires follow these injectors, replace. If 2 & 4 are still acting up Quad driver in ECM is bad. Also recheck the fuel fuse for injector driver.
If 2 and 4 are still not firing look at the new plugs for being wet or dry.
If wet you have either bad injectors that are leaking or dry not letting out the fuel.
It sound like you got bad fuel in the system but all injector would be having a problem.
What size are these injectors?? Are they low or high resistance ones? If you install the low ohm ones in a high ohm system ,you will burn out the drivers in short time. Have seen this happen. Weakest drivers go first.
Any way for you to do an injector flow test?? This would also tell alot about what is going on.
After you get this fixed you will need 2 new O2 sensor to have the motor running right. All that gas and running rich will cause wrong readings on the motor. Rick L. Ps Do you have the camshaft with the swap in this motor?? It's possible you have the wrong spark firing order?? I think it was a #4 & #7 swap. Do basics first to remove these issues. I have seen bad crate motors. SO don't over look this issue either.