Truck shaking and flashing check engine light at 1500 RPMs and 50 MPH?

When started just before takeoff or at slow down when RPMs reach 500, truck begins to slightly shudder. While driving at 50 MPH and 1,500 RPMs with overdrive engaged, the truck shudders. At 2,100 RPMs, the truck shudders. If you shut overdrive off it seems to get rid of the shudder most of the time, although sometimes it doesn't. At each of these times the check engine light will also come on and flash until you get to a speed where it is no longer shuddering.
I currently do not have a muffler, nothing past my cats. I've cleaned the throttle body, replaced the EGR, PCV valve, spark plugs, wires, and o2 sensors. After doing all of this, I ended up with a P0303 code. I changed the coil on cylinder 3, cleared the code, and drove to work the next day. Once I arrived home, I checked for codes again and the P0303 code was back. My main concern at this time is figuring out what is causing the shaking. Any thoughts to point me in the right direction?