Misfire after replacing ignition coils

A week ago my 2011 Gen 3 , 222,022 miles, started up with a loud knock that disappeared in less than five seconds. It drove fine and no other problems for that hour drive. Next day started up, knocking returned with some major engine shaking and CEL. Took to auto parts store to have code read - ignition coils two and four. Bought two coils that day. Tore down to the coils, realized the spark plugs are right there, bought four new spark plugs. So 4 new spark plugs and two new coils (2 & 4) installed. Started up, worse than before still has CEL. Did quick double check - everything looked reassembled correctly. Had code read, ignition cylinders and circuit. Decided to pay to have dealership diagnose it. They figured out the first cylinder was not seated properly, so no connection. They fixed that, cleared code, put it together. I picked it up and started the vehicle. The engine knocked and shook a bit then calmed down within fifteen seconds. I complained that it was not diagnosed/fixed. I was told the code was clear so it's good to go and the shaking noise was from the bottom panel that protects the engine being loose. The vehicle has not had a quiet ride since, but it has not sounded like it was going to die until today. Back to starting it (65 degrees outside temp), knocking and shaking. Code read, Cylinder 2 misfire.

So my plans: Switch cylinder 2 with another and see if that sounds better - diagnose if cylinder 2 was a bad one. Clean the EGR pipe. Then go for cleaning the full EGR and the manifold, including the four 1/4" holes.

My problem and what I need help with - I have been reading the other chats and watching the YouTube from NutsAboutBolts - but I am confused. Is it best to just do the EGR and manifold at the same time, or separately, to clean? Is there a diagram somewhere the shows the four 1/4" holes that need to be cleaned when the manifold is done? Has anyone actually tried the oxyclean soak on the EGR, or just using brake cleaner?

And is it worth calling the dealership and complaining? I know they did not do a full diagnosis and charged me almost $100 for it. If I would have a shop (dealer or other) clean out the EGR and manifold, what would be a reasonable cost? Is there anything else that could be making the misfire code trigger that I'm missing?

Thank you for your help!

 

Right now the coolant level is at full and I have not touched it, so no leaks from there so far.

I have not done a EGR circuit before, and I am extremely nervous. I do have a pressure washer, so I figured oxiclean to try it, then just go for it. I also have a pressure steamer, but I don't think that would do any better than the pressure washer.

All four spark plugs were rusted, and the two cylinders that were switched showed signs of rust on the sides. The other two cylinders did not look as bad, but we are planning on replacing sometime. I suspect water got in there at some point and from what I've read I'm not the only one.

 

I found a good picture of what the four holes in the manifold everyone has been talking about - so I don't need that anymore. Other pictures were always too dark and full of crud that hid them. I will be trying to do both at the same time, and will be going for it in two days. I will post with either victory or defeat!

 

I think the EGR was a problem. I didn't even recognize the valve AS a valve. I'm in the middle of cleaning now, and then it's trying to get it all put back together. I don't have a picture, but I am doing the manifold too. I

 

Here's the before and after pictures. We got the parts cleaned, dried, and put back together. When we started her up we had one big knock but then it stopped knocking, no shaking, and as acting like its supposed to. We drove it around town and on the highway without a problem. Figuring it was fixed, I took it for a 200 mile trip TDY. I dropped by a dealership and they cleared the old codes and warned me that there were two pending - one for unknown ignition cylinder misfire, and the other for evap leak. The next day when I was done with work the CEL came on. Today I was able to take it back in to have codes read and there was a total of 17! Misfires on 1, 2, 3, & undetermined/multiple, three involving evap (Iwas tokd its either a leak or blockage), and the rest were repeats. Did I just totally screw my vehicle by trying to clean it? Any ideas what is wrong with it now? My instinct is to check the hoses for any loose and that might solve the evap problem. We have not replaced cylinders 1 & 3 yet. Our problem is the vehicle is high mileage and trying to figure cost of parts & effort to fix vs trading it in at this point. Any recommendations?