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I have a 2001 F250 7.3 with a zf6 transmission. The "service engine soon" light comes on... then goes off... then comes on, then off, etc. Seems at random, although maybe a little more common at idle or when parked? I tried to read the codes with my bluetooth scanner and the torque pro app, but it said no codes were stored. I have heard that Forscan is a better app for getting codes, but they say you have to use it through your computer to really make it work. But I don't have a laptop I can use for that. I tried the forscan android app and it didn't work at all, I couldn't connect to the computer. But that might be the bluetooth scanner I have, I got the cheapest piece of chinese crap I could find (although it does work with the torque app).
I have heard of some cars that have codes store in the transmission or somewhere else not on the main computer, but I don't think these trucks have all that extra computers in them. At least, the manual transmission version probably doesn't (I hope).
I guess its also feasible that its some weird electrical issue making the light turn on for no reason, my right blinker light also doesn't work on the dash, but I find that unlikely.
The Android Forscan will give you all the codes you probably need. I have the Windows version on my laptop and have never never used it, although I keep telling myself to try it just to see what additional features may be on it.
Any tips on how to get it to work? I have my scanner plugged in but when I press the connect button it just thinks for a while before it says it can't connect.
There is a Forscan tutorial in the stickies section that has all the info to get you started. Also has a list of known working OBD2 dongles, because you're probably right about your adapter being your problem.