Truck is misfiring

While idle it shakes then stops repeatedly. Taking off it
shakes hard and has little power. Only from the initial start
of the drive though. It shakes a little every now and again
while accelerating. Once I reach about 45 while
accelerating normally it shakes really hard and my check
engine light flashes. I can get to the speed I need to and
the problem goes away after a little bit. Before I changed
the spark plugs if I let off a little and tried to speed up
again it would shake hard. That problem is gone. I get the
codes P0300 P0306 and P0135 (probably unrelated) I
have replaced the ignition coil for the 6th cyclinder, and
the plug and wires before the bundle look fine. Any
suggestions?