Knocking noise in engine

I started working on my friends vehicle listed above. All it had was a small miss a code for misfire cylinder 6 was present. I began by replacing all the spark plugs of course you have to remove the upper plenum/surge tank. When I started the car after the new spark plugs it ran even worse and still said misfire cylinder 6. I suspected either a bad coil or a bad fuel injector. I swapped the coils to see if it would jump codes to a different cylinder, no success. Then I swap the injectors. At first it popped up a code for cylinder 4 instead of 6. I thought yes I figured out the issue then it started running worse. Codes now saying it was misfiring every cylinder then I began to have a loud knocking noise. Now I start the car up an a really loud knocking noise is present. I have taken the car apart and put back together several times checking the spark plugs. I even replace the spark plugs with a different kind. I replaced one of the fuel injectors I thought was bad cylinder 6 and put one new coil on cylinder 6. Now all I hear is the loud knocking and then the engine shuts off. After picking my brain I thought maybe something went bad with the engine unrelated to what I did. Now my friend thinks I am the cause of the problem, the only thing that I could think of is that when I took off the surge tank/upper intake I noticed a black piece of half circular plastic that was loose in side when I looked inside I noticed that there were several half circle plastic pieces inside the surge tank that I assume used to direct air flow into the tank without separating the intake itself. I tried to put the plastic piece back in to no avail, I left it out and noticed also 2 other plastic channels misaligned and loose in the chamber. Could this be the cause of the knocking noise on the engine? I'm almost afraid something happened 2 the valves hitting the pistons this being an interference engine, but how would just changing spark plugs and the few things I did cause that problem? So now I want to go direct my attention to the intake an see if I could take it apart and repair whatever I see if that eliminates the knocking noise. I've been searching and searching for information related to this problem the only thing I hear is major issues. I am confused and frustrated that all I was trying to do is change the spark plugs and track down the misfire which I've done many times over on cars for it to result to this issue where it's not even drivable. Now my friend is very upset and I have been working hours on this for free. I did notice a few write ups for other people were complaining about similar knocking noises when they just change their spark plugs. I'm just really hoping this is something minor, and not only will I have to try to make my friend understand that it was nothing I did but even then it doesn't fix his vehicle and might need a major rebuild. All fingers are pointing to me because I touched the car, it was supposed to be a simple fix that I've done a dozen times before on other vehicles and now it's turned into a major pain in my butt. Lol. Sorry for the long explanation.