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I just got a rebuilt 4.2 in my F-150. It is mostly working, but at idle and when putting it into gear, starting from a stop, etc. it hesitates and runs rough. Sounds like it is going to stall. Once I get moving it sounds fine. Just had a shop run through anything they could think of and had it hooked up to a code scanner.
It shows intermittent missing, all o2 sensors are giving readings withing the right range. They are suggesting possibly EGR valve or cam sensor. If it is cam sensor, wouldn't it run rough at all speeds? Would a bad EGR produce these symptoms?
In any case, they cleared the computer and told me to drive for a couple days and see what comes up. They also complained about the 97 computer not being descriptive enough.
I would ask them how they lined up the cam position sensor/synchronizer assembly.
It has to be done right or you can get symptoms like you have.
Chances are pretty good that only your dealer has the tool needed to do it.