Here's my situation,

I have a 2003 Escape V6 that seems to stumble when I get the car above 40 mph. On top of that it seems like there is something holding the car back from accelerating as the tachometer will climb with the acceleration, but drops back down to around 2000 and the engine will start to stumble or lack the power to accelerate. Below 40 mph (and driving around the neighborhood streets when the tachometer is around 2000), the car seems fine and the idle seems okay. When I got the car home, I used a scan tool and got the (pending) codes P0301 and P0316. My CEL did not come on during the drive and the scan tool doesn't read it as being 'on'. So far these codes are telling me that I have a misfire in the #1 cylinder and a misfire withing the first 1000 revolutions of the engine. So far I have changed out my spark plug, swapped the ignition coil, changed out the fuel injector, cleaned both quick disconnects for the injector and the coil and changed out my upper intake gaskets. Each time doing a test drive of at least 10 miles or more on neighborhood streets and on the freeway I keep getting the same (pending) codes P0301 + P0316 with the same stumbling reaction from the car during the test drive and no CEL that comes on EXCEPT for the last and most recent test drive. The CEL did come on briefly for about 10 seconds and it was blinking, but it went away. By the time I got home and scanned it, the reader was telling me that the CEL was in a 'non illuminated' or 'off' state. Something is telling to look at the wire harness leading to the coil or the PCM. What else am I missing? I am just getting tired of taking of the intake manifold and putting that back on only to get the same fault. Any help would be greatly appreciated.