First lets tackle the poor running. If water got inside the cap and you tried to run the engine, the arcing would likely have caused carbon tracking. You can try scrubbing it with a rag but your best bet will be to replace the cap and rotor. That system is capable of producing very high voltage and any residual carbon tracking is going to cause misfires.
If you removed the spark plug wires from the ring that goes on top of the cap, you'll need to find top dead center on cylinder #1 on the compression stroke, then look where the rotor is pointing under the cap. That's where spark plug number 1 goes on top of the cap. From there, put the wires in the firing order, 1, 8, 4, 3, 6, 5, 7, 2. Cylinder 1 is driver's side front, then working back they're 3, 5, and 7. The passenger side, front to back is 2, 4, 6, 8. I think your distributor turns clockwise as you're looking down on it.
Once it's running smoothly, you'll need a timing light to properly set the ignition timing. You might also be able to see the "witness marks" where the bolt was tightened previously. Set the distributor to the same place for a starting point.
Saturday, April 14th, 2012 AT 7:09 AM