Has anyone suggested checking the grounds for the engine? The stock ground wire is hooked up to the driver's motor mount and goes to the frame rail. You may want to add another ground from the passenger motor mount to the frame on that side.
I'd also check the power connector on that side. Isn't there some sort of a capacitor attached to the side of the coil mount? I'd also check where the coil mounts to the bracket, make sure the screws are clean and tight.
EDIT: The ground wire can get corroded, might be worth replacing the ground wire completely. I replaced mine with one I got at my local parts shop, it was in the battery section. Dunno what gauge it was, anyone have a recommendation?