1998 Rodeo Mis-firing

My 1998 Rodeo (65K miles) has had its share of problems since I purchased it. There were several re-calls to fix various things from engine
mounts to an insulating plate behind the cassette player.
Last winter, with the car running poorly and idling terribly, the "Check Engine" light came on and I took the to a dealer. The dealer discovered the manifold intake gaskets needed to be replaced along with two oxygen sensors. Some of the work was covered under warranty, but over $600 was not.
A little over a year has gone by since that problem, and like clockwork, another has arisen, been temporarily fixed, and then reappeared.
A few weeks ago, the Rodeo was running and idling terribly, the "Check Engine" light came on a flashed, indicating a mis-fire. A mechanic I trust said cylinder 6 was mis-firing like crazy and when he opened it up, there was a good bit of water inside the cylinder! The plugs and coil all checked out fine and he got rid of the water and the Rodeo ran and fired properly.
The mechanic said the water could not have been from water in the fuel. Is this true? He said the water entered the cylinder either by running under the hood somehow or possibly from slamming through puddles on wet roads. Sounds like he's reaching, to me... Could this be another failed gasket or seal?
The "Check Engine" light stayed off for three days following that bit of work, and now the Rodeo is doing the exact same things it was doing before: Running and idling terribly, and the "Check Engine" light remains on constantly and flashes when the mis-firing is really pronounced.
I'm at a loss as to how I should proceed. I'm praying that some knowledgeable Isuzu guru and offer either a off-the-cuff diagnosis and/or a good way to proceed with fixing this car. Might any of this be covered under warranty or will I be stuck with another giant bill?
Thanks, Justin
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