There are a number of you that posted threads regarding misfirings and EGR related engine codes. I was chasing the dreaded P0401 (EGR flow insufficient) also and came to a revelation. I checked the EGR valve (held 15 in. of pressure), EGR solenoid, DPFE sensor and vacuum lines and everything was in working order. I then realized there was more to the problem.
What I didn't understand was there was no misfire codes registering. I noticed that when I pressed the gas pedal abruptly, there was a slight hesitation. When driving under a load, the vehicle shuttered and hesitated between 1500 - 2000 RPM. Since the vehicle had over 120,000 miles, I replaced the boots and spark plugs. However, the problem persisted. I spoke to a Ford technician and he informed me that this may be the sign of a bad coil. So I did a little research and found that coils can range from $60 - $150 each, depending on the brand. I checked eBay and hit the mother load! I bought 8 coils for $115, S&H included (see pictures for part numbers).
You may ask "Why don't you just test them all and buy one instead of all eight"? I personally felt the investment was worth it since the truck was 10 years old. Besides, the amount of time it took to check each one would have been the same as simply replacing them all. I began replacing the driver side coils first because they were the toughest due to the fuel rails (I just loosened the rails and was able to replace coils #7 and #8 a bit easier). It took about an hour and a half because I lost a socket that I needed. After replacing the coils, the truck ran like a sewing machine again. I cleared code P0401 and it has been back.
I assume that you can have a coil misfire and not get a misfire code because the voltage was not enough to throw a code. Not sure why the EGR codes came on, but they're gone now and that's what counts. Tell me it this helped.