Multiple misfire codes

I was driving my vehicle with absolutely no
problem. I slow down for a vehicle that was turning
and went to hit the gas, slowly accelerating I could
hear a knocking noise and then I had a loss of
power and pulled in to a parking lot. The engine
started shaking and the error codes were P0300,
P0304, P0306, and P0316. I had it towed home and
checked the spark to all ignition wires and the coil
pack with a tester and it lit up every time on all 6
wires and coil ports. I changed the spark plugs and
the crankcase position sensor and I'm still getting
these codes. I've gone all through the engine with a
flashlight and I can't find any damaged wires or
vacuum leaks.The fuel pump was replaced 2 years
ago but when I turn the key on I can hear it
activate. What could this be because I can't find
anything online. This is a 2003 Ford Explorer Sport
Trac truck with a 4 L V6.