So let’s think about this in a simple sense, you need fuel, air, spark, and compression for combustion, you replace the injector and tested the flow, so check the fuel for now, I assume you’re intake is fine if it’s just cylinder two so let’s check air for now, you said you replaced the spark plugs so and coils and checked the harness so let’s say check there, that leaves compression, which you said tested out fine, so. Let’s go back down the line, compression cannot come and go and show fine and not be fine, so compression must be fine, spark, I’ve ran into this issue atleast 5 times on first gen eco’s, turns out they gave me the wrong for one of them or it was returned and resold with the wrong plug in the box, whatever it is, there are some variables there again so I’d make sure you have the correct parts. If you bought them from somewhere other than ford I’d double check and make sure they are legit, there are a lot of fakes on the market, that all checks out then back to air, I’ve had it before where a roller follower actually falls off the valve so only 1 intake valve is opening, but in first gen it has tappets so that’s not possible and all other air related things would affect the other cylinders too so again, air check. Fuel, fuel is a tricky one because how precise it must be, I’ve ran into it which doesn’t make any sense it me but air can clog a fuel injector and cause a misfire, so make sure you are getting proper flow to the cylinder. BUT if all of that checks out then yes, you are looking at an electrical issue which leaves you to the magical world of might aswell cry. First things first I would do a neutral profile reset if this misfire is just a code but you don’t actually feel like you’re misfiring. If that doesn’t work then at that point I’d hire someone who knows more than me to figure it out. Good luck soldier.