For some reason, I was thinking yours still had a single coil. Sorry. From your symptoms it still sounds like a bad coil (s).
Some cylinders misfiring on a engine will affect the engine more than other cylinders. It's has do do with the was cylinders are phased in the firing order.
A bad coil(s) on yours could still very well be the problem.
These are kinda hard to diagnosis, but if you have a catalytic converter stopping up, it may act like your problem. Someone that has a scan tool and knows how to read the live data can usually look at the O2 sensor data and determine if a converter is stopped up. Not always, but often it will throw a code of "low efficacy" for the converter, ( though that tends to be another problem than a bad converter)
Another possibility, if you have trash in your fuel tank, while you drive, sometimes debris will be sucked up around the screen for the fuel line and starve the engine for fuel. You stop and it falls away. You usually have to drop the tank and clean it out if that is the case. I don't think this is your problem though.
Here is what I would do.
Replace the coil you saw arcing.
Add 4 or 5 cans of Seafoam if your 1/2 a tank or more fuel of fuel. This will help eliminate water AND clean the injectors. 1 can will not do anything in that big of tank.
If it still acts up, Get someone to scan the system and look at the individual cylinder misfire chart.
Say #8 shows miss fires.
Plug the plug Does it look fouled (black carboned up, wet)
You said you replace the wires. (hope the were the cheapest Autozone ones). They are crap. You may have fixed the problem with wires and just need to replace plug that was damaged by bad wire or coil.
Any cylinder that shows a misfire in the data chart needs attention.
The things that affect a cylinder fire are: (Keeping in mind your symptoms) Runs ok for a while starts missing pulling grades, looses power, stop cool off and runs ok a while
Spark Plug
Spark plug wire
Coil
Fuel injector.
Missing pulling a grade means some thing in the electrical side of the ignition is breaking down under a load. Plugs, wires, coil
Fuel starvation might also cause it. Maybe
O2 sensors should be reading "lean" if this is the case.
Did you replace the fuel filter?
Do that if not. Those filters are good for a max of 30,000 miles. Crappy gas, 12,000 miles or less.
As diagnostic scan to will tell a tech where to look if they know how to read the data.
Without throwing a lot of parts that are not needed. It's sad but there seem to be less and less Techs that know how to properly diagnose problems today.
They see a code and throw a part at it.
