You nailed it... water really IS getting into the engine! Hi, my name is XXXXX XXXXX welcome to JustAnswer!.

As time wears on and vehicles tack on miles, this problem is now becoming a bit more common. Shoddy weather sealing and water management in the wiper cowl area above the engine allows water to spill over the intake manifold area and is then sucked in through leaking intake gaskets. Seepage seems to be pretty consistent from cylinder-to-cylinder, so small amounts of vacuum leakage doesn't affect idle quality for the most part... unless it's sucking water instead of air.

The intake manifold on your Hemi is plastic and uses eight formed rubber gaskets that sit into recesses of the intake manifold which is bolted directly to the cylinder head. For reasons I can't explain, ONLY the 2004 Durango has been afflicted with misfire from leaking gaskets, but it may have as much to do with water management as it does with vacuum sealing.

To verify this, use a spray bottle or garden hose to introduce water to the base of the intake manifold in small quantities as the engine idles. Misfire will occur when water is aspirated through the very small leaks that have developed between the intake and cylinder head. A fresh set of gaskets will take care of the problem... pretty much forever.

As for the water management issue, check to see if you have any missing, torn or misaligned weather sealing in the cowl-to-hood area. A little leakage here doesn't really seem to be a problem unless the intake seals also happen to be seeping.

Let me know if you have any questions. I'll be glad to help.

Thanks,
Ed