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I have recently purchased an 04 F250 crew cab with the 6.0 power stroke, it has a cold air intake, 4inch exhaust from the turbo back and has a program in it but programmer didn't come with the truck. When I sit at a traffic light and go to leave on a green light the truck kind of hesitates or acts like it's missing out( maybe loading up) shoots out black smoke then runs fine, it doesn't do it at all the stop lights but does get irritating. If I get it flashed back to stock settings will the truck run normal with all the upgrades? Any suggestions?
Yes it will be fine if you have an egr delete it may trip the check engine light with the new stratagey. still the only thing you can do would be to take it to ford and have them reflash it back to the lastest strategy. How do you know it has a tune and do you know what kind or what tune? Depending on what kind of tuner is in it it may make diagnosing the actual issue difficult since some of them trick sensors into seeing numbers that aren't really happening. Any codes, pending codes or anyway to read them? Your best bet I think would be to check for codes just to see if there are any then have it reflashed by ford then if you want to run a tune after you get your issues figured out get an SCT tuner.
What kind of diagnostic capability do you have? Ultimately you're going to need some kind of scanner or gauge setup to run through the OBDII port, it's very much a must-make purchase. If you go to the 6.0L forum, you can get all kinds of recommendations on what kind of setup to get: 6.0L Power Stroke Diesel - Ford Truck Enthusiasts Forums
But in the mean time, if you have a multimeter we can get you started. For rough running, the easiest thing to do it load test each battery separately, and make sure they're not going out. Weak electrical is a huge problem on the 6.0L. After that, you need to test the FICM: https://www.ford-trucks.com/forums/8...procedure.html
If the batteries are shot, or the FICM shows less than 45V, you should get the alternator tested.
After that, since the injectors are oil actuated, I'd recommened putting in new T6 5W40 oil, and making sure you have the correct oil and fuel filters and the correct caps. It sound's like a simple thing, but some non-OEM filters (specifically Wix and NAPA) come with a replacement cap that doesn't fit correctlty, and mixing filters with wrong caps is even worse.
To wrap it up, at this point I'd say test the electrical, do the basic maintenance workup, and as soon as you get a gauge setup start trying to pinpoint issues. Reflashing the truck back to stock won't cause you any problems, but if you wanted to wait until you check the FICM, there's a company called Power Hungry Performance you can send the PCM and FICM to and have them reflashed to a stock-based but improved software flash.