Codes P0300, P0308, P0345 and P0349, when stopping at stop sign the check engine lights start to blink and I hear a loud knock coming from.

The car was running lean due to a performance cold air intake it had because it required a tune. So, I removed it and replaced it with the OEM intake. But my issue with the vehicle is that when I go on a cruise and am speeding and accelerating fast and when I get to a stop sign the check engine lights starts to blink and I hear a loud knock coming from the engine and when that happens the car loses all power for like 5 minutes, but after 5 minutes the check engine stops blinking and the car goes back to normal. This problem happened when I had the performance intake and is also happening now with the OEM intake. I was able to scan the codes and I got p0300-p0308-p0345-p0349. I have also replaced the camshaft sensors before I got help from this website to locate the position they were in and I changed them out, also ford put a whole new PCM system in the vehicle, but they never mentioned anything about the engine knocking when I accelerate the car a lot. The car is also back on stock tune. I hope I can get some help from here. Thanks