Number two cylinder misfire

If it ran okay but then through the fault was that with the new coil or original? New plugs or the ones that were in it?

Well, with a new coil and plugs the next step would be to actually flow test the injectors, or a test by swapping the one in cylinder 2 over to another cylinder. That would also let you look at the part number and see which ones it has in it. You already did the compression test so I would say the valves and such are okay. Not much else that can cause a misfire left.

Okay, if the plug was wet that injector is likely bad. The black is from excess fuel and it sounds like it is sticking open. OEM number for the injectors for the 2.0 is 35310-23210.
So I think you found the culprit. Because the other plugs looked dark as well I'm going to say someone stuck a set of salvage yard injectors into it and were not real particular about what part they used. Then one of them failed and is dumping a lot of extra fuel into the engine and that is also why the trims are so high, it is trying to lean out the mix because of the extra fuel. I would probably replace all 4 with the correct part numbers and do an oil change as it's very likely the oil now has a lot of gas in it.

That would do it. If even one injector is dumping fuel it will signal that the engine is running rich and try to lean it out. You mentioned some cleaner in the fuel, it's possible the cleaner did it's job and flushed the dirt out of the system and it got stuck in the injector and is preventing it from sealing, It would still click and open but because of the fuel pressure even being open half the thickness of a hair will cause it to flood out.
However as the injector you pulled has the wrong number it's likely a combination of things all coming together. The plugs you put up earlier all showed signs of running rich an if the problem was only the single cylinder then only that cylinder would be carbon coated. At this point I would opt for replacing the injectors, If you had a way to flow test them I'd go that way but a flow bench isn't a common item in most places. Plus with the cost of a set of 4 new injectors the testing would cost more than replacing.

I would suspect that more than one is flowing fuel. I would clean all 4 if you can and then see if they are sealing, look at the O-rings real close as well. I see sets of 4 of the OEM part number for under $150.00 online. Take a look at Rock Auto if interested. As for number one causing a misfire code in number two, that could happen if the firing order was different but I suspect you have more than one injector acting up.
Okay, that sounds like a plan, If you have a way to cycle them like an injector tester to see if they act up in use you might find a couple are binding.

Great to hear it runs. Okay, it looks like you answered your own question about the TPS. If your scan tool can graph the data you can watch the TPS voltage and slowly press the pedal down. If it's got an issue you should see the voltage drop out, just go very slow as the data has to go through the network and that time lag can hide a momentary drop.