Check the compression @ each cylinder, and the 2 intake gaskets.
Try swapping spark plugs from side to side, then wires (if one is too short to do this, temporarily use 2 known-good wires off of something else, a V-8 engine, for example).
Swap the wires between the two terminals on the coil. (Yes, this will work, they both fire at the same time and wire location is NOT specific.)
Does any of this make any difference in how it runs?