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Okay, so you definitely have a bad ground. Likely a cheap/free fix. Look at where your computer (pass firewall corner) is located, and locate the grounds from that main harness. Those are known to corrode, which can cause the engine to run all ratty, and also cause other issues. In fact, spend a couple hours and check all your grounds. The ground strap from engine to vehicle (braided steel) is also a common issue. Def cause a rough running engine.
 
Start off my removing your battery terminals so you don't short anything. A steel bristle brush, emory cloth or med-grit sandpaper, brake-kleen and some rags help. Then...

Well, the engine ground strap (braided, flat, steel "belt" w/ ring terminals on each end) SHOULD go from the back of your cyl head to the firewall, I BELIEVE. For the battery, obviously you want your post/terminal to be REALLY clean. DON'T use coca-cola, it'll work but makes a sticky mess. The parts store should have a can of batt terminal cleaner for like $5. Follow the cables from the negative post to the fenderwell, and follow the other one down to either your frame or engine. There is also a ground from the alternator to the engine, that's pretty straightforward.

The PCM, located behind your coolant reservoir (remove this to really get in there easier), has a harness with an 8mm bolt in the center. Remove that and check to make sure there's no contamination or corrosion. You'll see there's like 80 wires going into that harness:eek:. You'll have to just follow the black ones to ground. IDK off top of my head which ones, or where they go, it's a matter of patience. A razor to cut open the wire loom (be careful not to cut wires) and some electrical tape to re-wrap it after you're done are a must.

It's still possible that I'm wrong and that your grounds are fine, I've just seen bad grounds throw a good mechanic "under the bus" so many times...
 
And just to add, if you see any melted wire looming while you're in there, I'd open the loom and inspect the wires. Like around your exhaust manifold, etc. If the loom is melted or covered in lots of greasy buildup, the wires inside could be compromised, cracked, or broken.
 
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