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Are there any ticking noises from the top of the engine from around either valve cover area when the engine is running?
These engines are known for rocker arms, now called followers because the push rods are no longer used. Your engine has 2 intake valves per cylinder. And is one follow is failing, one valve will not open properly and cause a miss fire as you describe. Also, the lifters, now called tappets, are prone to collapsing and cause the valves to not open fully which will also cause a miss fire. You will have to remove the valve covers to inspect them.'
Also, valves sticking in the valve guides. Basically items limited to a specific cylinder, not all of them. Since you are only getting miss fires on cylinder 1 and cylinder 3.
Have you done anything with the fuel injectors?
Then, the problem is mechanical. You have replaced the coil, injector and spark plug.
I would look at the valve train under the valve cover on the passenger side. Check the cam lobes for scoring from a failing follower. Also, when the engine is cold, check the followers for looseness compared to the other ones.
It could be, but they usually take a while for the leak to seal once the engine warms up. Like the intake gaskets. But you would have to drive it for about 20 minutes for it to seal.
Your very welcome. Thank you.