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We need to know the trouble code stored in the computer memory, to be able to narrow down the alternatives effectively. There are too many possibilities in a modern car to just start guessing and throwing parts at it. You can have teh codes read at just about any auto parts store, usually for free.
The catalytic converter (or O2 sensor) would trigger it's own codes if it was acting up, it would not cause just a misfire code. They are separately monitored.
You said the coil pack has not been replaced. That is a common source for misfires, especially when it's a random misfire instead of consistently in one cylinder.
Plugs and wires were a good idea to start with.
A random misfire could be a result of incorrect fuel mixture too. If you had an intake air leak that leaned the mixture out too much (as it sounds), it could technically cause misfires. The O2 sensor should have noticed the lean condition and trigger another code for that. Hmm. Maybe it wasn't done in 2001 yet, now I'm not sure.
If you drove with an air leak and misfires for a loing period of time, it could possibly have caused the coil pack to fail intermittently. They don't fix themselves either.
Look for more air leaks on the intake side still. Glad you found the crack.
My vote is on the coil pack, but I admit it could be something else too.