Engine Missing
 

My engine has been missing lately, but it runs fine otherwise. Here is a link to what it sounds like at the exhaust and the engine.


I cleaned the MAF, checked the IAC, and replaced the thermostat so far. I have plugs and wires next. Anybody have any ideas as to what it could be?

Yes, do the spark plugs, my '94 4.0l needs a set every few years, use autolite or motorcraft, other brands don't seem to last in the 4.0l.
Check each gap, 0.054 is spec
For the '97-'00 4.0l OHV use Motorcraft part number is SP500 (Platinum) (old part number is AGSF22PP) or SP413 (Premium Nickel)

I only changed original wires in 2010, 16 years old, nothing lasts anymore, lol.

Also run a can of Seafoam in the gas tank, $8, I do this once a year and seem to get less random misses, but I use cheap regular gas with no additives :)
Over 300k on my 4.0l now

Nice! I got the motorcraft plugs because I heard that the 4.0 can be finicky when it comes to plugs. I've been looking for Seafoam because I heard that it works pretty well, but I haven't found any yet.

walmart sells seafoam bought some yesterday

If you replace the plug wires watch the firing order on the drivers bank:
Coil pack
3 4
2 6
1 5
front

It is easy to reverse two of those 5 6 4 wires

Would the gap of the plug have any effect on the engine? I hear varying thoughts on this, but the gap is supposed to be .054, and the ones I bought are at .040, so there could be a chance that the previous owner didn't check the gap of the plugs.

That's too small a gap, yes you would get misfires with that.

General "rule of thumb" for spark plug gaps is that you can change them but no more than .01, so for 0.054 range would be 0.044 to 0.064.
I tend to just go .005 up or down, so 0.049 to 0.059

But why change the gap at all..............well there are reasons, lol.
If you are a conservative driver you may want a slightly larger gap for a hotter spark at low RPMs(0.059), this can improve cold weather starting, and MPG at low RPMs, but when you get above 3,000rpms you can start to get misfires with the larger gap as the coil recovery time is shorter and can't build up enough voltage to spark the larger gap reliably.
Larger gap can also help if you are burning a little oil on a high mile engine.

Smaller gap works better if you are at higher RPMs most of the time, but can cause misfires on cold weather starts with rich mix.

The factory gap, 0.054, is not the optimal gap, it is the average gap.
Best thing, if you want to re-gap, is to change it, then drive it for a few weeks and then pull out 2 spark plugs, see what they tell you about combustion, nice light brown electrode is what you want to see.