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Pull the valve cover off and look for something weird.

Plug wires in the proper place? Lol
 

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Did it run before? I know you had issues with bad injectors, but did it run after you replaced them?
 

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It hasn't run right since before the original injectors. I pulled the original injectors to see if any were bad. I had them tested and they were fakes. Surprisingly enough; the car ran well with the fakes.
I did have issues with backfiring when getting into boost or possibly just higher rpm's?
Swap the two injector plugs.
 

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If both 5 and 6 are acting up; what will swapping their injector plugs tell me?
You repinned some of the 60 pin connector right? Some of which were fuel injector pins. Maybe they got switched.
 
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I ran an injector pulse test with Tuner Studio twice. The correct injector clicked each time.
Do you have a video of it running right now with the issue? If fuel is getting there, spark is happening, and compression is good that really only leaves limited options as to what may be wrong.

There could be something in the valvetrain, but I’d expect it to have made some type of noise before knocking out 2 cylinders - if that is the issue.

I have the video of when you got the car running initially, and everything sounds good. So at one point everything was fine.
 

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Here's where I'm at... while idling; I pulled #5 injector plug and heard no difference in idle nor did the tach show a drop. Yet; the cylinder is reading the same temp as the others when I shoot it with a temp gun. It's things like this that make me hesitate to take everything apart just yet. I've been hot rodding for 40 plus years and never have I had so many issues with runability until I got into 5.0 Mustangs.
Yes; I'm whining. :(
What’s the temp of the cylinders? The two bad ones and good ones.
 

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350-400 give or take.
All the header primaries measure the same, Even the ones that aren’t firing? Did you measure a couple inches away from the flange?

The bad cylinders will be under 200* if you start the engine, run In for a 15 seconds or so and then check. That is if they’re not firing.
 

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If you have 7/16 studs, you can give the poly lock quite a bit if torque. Half a turn on the adjuster and set screw, back both out 1/4 turn, and then lock it down using the outer nut.
 
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