I got a 172 and a 179 code from the pcm which from what I can tell are related to the o2 sensors or the miss/leak, BUT I did find a bulletin on a hesitation/surge/misfire that is related to the pcm and requires the pcm to be replaced or reprogrammed!!! that sounds really intimidating and I don't know how I would replace or reprogram the pcm if it's anything like reprogramming a pcm on a gm car where you have to hook the test connector up to a computer and wait until it is done...another one of the benefits of working for a gm car dealership, the principals are the same, but access to ford special tools is next to impossible..

 

If there is a leak, I'd fix that first. Then you can clear the code and see if they come back after you run it a while. If they come back then you can worry about reprogramming or replacing the PCM. The reprogram should be similar to what you are used to with the GM's. If you choose to replace, you may be able to find an cheap one at a salvage yard.