The first place I would look would be the wires once more.
Look for any place they might touch/ bounce onto metal. The holders are not spaced enough to keep the wires in a safe zone.
My niece has the same vehicle (It was a 2003), they checked the wires and they seemed okay, when it arrived at my house in after dark, It was plain to see that it had three little lights (arcing) off of the wires.
With a decent look at the wires they did look normal, however, with a closer inspection at the arcing areas of the wires, you can see a faint gray spot on the wires.
We replaced the wires and obtained a few feet of 3/8 fuel line (I had on hand). I split the fuel line and cut it into various lengths to cover sections of the new plug wires where they were close to metal parts.
Before you run out and purchase new wire, one might swap the two wires in question with two others (providing the lengths work out) and see if the missing stops.
Other than that, my next guess would be the coil.
Here are some other things that you may have overlooked on our site. "Repair Guides" are found at the top right of our pages. Here is a short cut to get in there. Look under the "Engine" section for additional aids.
https://www.2carpros.com/articles
Unfortunately, the niece was "T" boned by a "texter" and rolled the pony three times about a week after the fix.
Keep us informed.
The Medic
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Wednesday, June 6th, 2018 AT 7:45 PM