You know that you don't get multiple cylinder misfire codes from a maf right?
How are your plugs and wires? Probably have carbon tracking like the last 6 cars I diagnosed at my shop for misfires. If that is the case you HAVE to change the plugs AND wires.
The O2 codes will most likely be a result of the misfire, but the 396 code (maybe coil driver??? dunno)I don't know off the top of my head like the others so you might want to search on that one.
I have also run into a fair amount of coil problems, if those coils are opposite each other which I think they are you may have a bad coil. I would just take the front cover off and the imrc (just let it dangle) and with it running pull each of the 3 front plug wires off (one at a time only) about 1" or so away from the plug (enough to hear the snaping sound of the spark) then put it back. if one or more is dead on the front 3 then odds are you have a bad coil pack (replace the coil pack). If all 3 test ok then this means you probably have the earlier mentioned problem so replace all plugs and wires.
There are other possibilities but thats the most common that I run into on a day to day basis.
98 Contour SE 3.0L 5-speed
SCT PRP, Gutted IMRC's, Fidanza Flywheel, Race Ported 2004 3.0L Oval Port, Zex 125hp shot, 70mm Mustang TB, 42Lb injectors,Walbro 255 pump, Traction Bars, Zeitronix wideband o2, lots of little things, 10,000K HID's!! 
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