When you are in CAT ET you will go into WinFlash - it is an icon on the top of the screen that looks like an ecm with an arrow going into it. Once you are in WinFlash, you will choose a file using the browse button. There are flash file disks or you can get files on here for the application you are looking for. Once you choose the file then you click on the begin flash button. A status bar will come up telling you that the flash has begun and will move from 0% to 100%. Once the flash is complete a window will pop up asking what you want to do next. Choose RETURN TO CAT ET. It will then reload your information from the ecm. You MUST program the personality module (just above the FLS and FTS setting). Just choose to program it, the program will ask you if you are sure, choose yes. This is where you will need to use the keygen to make the password. If your keygen fails to make the right password, then you are stuck at that point. This is why you will have to flash it with a wash file first, then with the desired file that will get you past the three didget interlock code problem. It is done the same as described above.
Once you have completed the flash, always check your file by starting the truck and checking throttle response. You can flash an ecm and the truck will start and run, but with out the personality module being programed properly, you will have a dead pedal.
Any time you flash an ecm you should use a break out harness and go direct to the ecm, not through the data port as you can end up with corrupt files. I have had some older trucks where the flash would not go through the data port and would reject or freeze up half way through. Also it is much faster to use a break out harness.
Hope that answers your questions
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