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Lets slow down everyone wow....
wiring harnesses, reflashing pcms etc.
If you reflash your pcm and you have modified injectors you just screwed yourself. You need to get a monitor on that truck and see what all the codes are and work your way through each one. For example there is a common issue with the fuel injection control module (FICM) where the harness has some rub spots common on the 6.0L and the harness connectors under the FICM not being connected all the way/ ziptied because the clips broke. That could be causing your injector codes.
Also the boost issue is common with a dirty turbo. The turbo is not like older diesels its a variable geometry turbo (vgt) and if the fins on the unison ring are dirty, bad, rusty from a previous headgasket issue its common for them to stick and cause high/low boost issues. I would start watching dieseltechron's vidoes on youtube on how to monitor and what each sensor should read and how to track issues when one isn't right.
A very common monitor is a usb to obdII adapter for a laptop and download the forscan software (free) or a scangauge, or edge insight monitor. They are worth their weight in gold for especially a 6.0L owner. Do some research and don't go throwing money at anything until you watch some dieseltechron videos and do some googleing. There is a section on this forum that is called owning a 6.0l or what to look for with a 6.0L do some googeling and trust me you will begin to understand the strengths and weaknesses of the 6.0L.
-99 F250, 4X4, 6.0 trans cooler, 08 mirrors, 05 grill, AIS Intake, lvl kit, JW Vbody, cncfab hpop lines, WW2.
04 Excursion Modified, 04 F350 Modified, 06 F350 Modified
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"Its like me getting five 5 gallon bucks and throwing regular, mid, premium, #2 diesel and offroad diesel and then shooting a roman candle at each one to show which ones burns better."