A flashing check engine light, is showing you it is about to set a code in the PCM. If you don't have access to a scanner to retreive the codes, you can go to local auto parts store.
Your big chain stores like Advance, Auto Zone, O'Reilly will do this free for you. We would need the code numbers to really help you, everything else would just be guessing.
Flashing CEL usually means a hard misfire, which could damage the catalytic converter.
I bet you have some P030x codes in the ECM. You have to get a computer diagnostic to see which cylinders are misfiring.
if it's running rough try using a different grade of fuel, I read the manual and they tell you that 87 octane runs the truck smooth, if you can find it run "seafoam" for the next couple of tanks, the stuff is 10+