Ford 2.3L with 312k miles has ignition problem

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Comedy (?) aside, my son was driving my 1997 Ranger 2.3 "Lima" with 312k miles. Told me it wasn't working, so we went and got him. I was able to start it and get it going, but it had a miss and would die or nearly die at stops.

I limped it home a couple of miles into the driveway.

Come along with me on a troubleshooting journey!
 
Anyway, little history on the Ranger. At around 270k, I put a junkyard head on it. This fixed a problem where it would die after you revved up the engine. Weird problem, seemed to be because of recessed valve seats and the lifters pumping up when you revved.

Just recently, it got a leak in the catalytic converter and I had bought a replacement converter pipe but hadn't put it in yet. So a noticeable exhaust leak. It was smelly when I drove it, but maybe that was because of the leak.
 
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The check engine light was on, so I read the codes as soon as I got it home. P0303 - cylinder 3 misfire.

Something interesting about this engine is it has two spark plugs per cylinder.
 
Regarding ignition, it has two coil packs - each one serves all four cylinders. So it's a robust setup with a lot of redundancy.

Here are some more clues. There is a damp area around the exhaust on cylinder #3. The oil looks clean. (This engine uses very little oil and the oil always stays clean.) Plenty of coolant in the radiator and overflow. Coolant looks good to me, not obviously contaminated.
 
I got a compression tester and started last night, but I was being lazy and didn't remove all the plugs, so I don't think it told me much. Got about 125 on cylinder 3 and 2.

Today, I decided to do the compression test correctly. I removed all four plugs from the exhaust side, easier to get to than the intake. Shown below, #4, 3, 2, 1 from top to bottom.

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I was going to explain the steps I used to identify and solve the problem, but after moderator involvement I don't care to anymore.
 
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