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Long story short I have an 02 7.3l with 155k on it and was driving normal at 65 mph and all of a sudden it had no power and was running really rough. Pull over and shut it off unplugged my ts tuner and it fired right up ran fine for a few min drove down the road normal.. and then fell on its face again.. no acceleration.. no power like a misfire.. or dead cylinder. Check engine light on .. would run fine for a few kin then again.. shut it off fires right back up and drive again.. now it only runs ****ty..no codes from local computer. Buddy has Ford laptop and forgot the codes bit said #1 injector fail or no contributing etc.. and trans sensor that's all.. so I ran it.. pulled the plug on 7 and made a sound change.. same with #5 and #3... but unplugged #1 and no change.. so I said the the hell with it and replaced all 8 with stage 2 from full force and valve cover harnesses got it started.. same ****!! Rough idle no power... but not as bad as I have seen on YouTube for bad idm that was bad.. only like 1 or 2 cylinders are not working.. full level at 3/4, CPS changed, no chip in it, oil level good.. is the idm bad? Ford computer does say idm is bad.. and normal blow by... one odd thing is.. is that sent my chip to be reprogrammed for the injectors.. and they said it was fried and wouldn't take a flash and had to buy a new one.. ?! Makes me lean more towards the idm since the chip is fried.. i dont have a way to do a compression test ... please help..
Keep your keys far away from the ignition switch when messing with a chip on the PCM, classic way to fry stuff. Symptoms sound like bad wires and connections to the injectors. Commonly throws a P1316 code and the IDM shuts down the bad bank. The new under valve cover harness is part of the equation but also the harness connections on the outside of the VC and the gasket itself can have burnt and melted pins. Search for '50 cent mod' and you'll see threads with good pics of what to look for.
Another common harness issue is at the 42 pin connector. The underside of the harness rubs on the driver side valve cover, eventually rubbing thru and causing intermittent shorts.
Nothing against TS tunes but there are better out there, especially considering your hot new sticks.
As you found out many code readers do not work on these engines. You can get an OBD adapter and an app like Torque Pro or ForScan for not much money, then you can read the codes and watch a bunch of sensors in real time. Great for diagnostics.