Check engine light

For the past several weeks I've been having a problem with the check engine
light on my 1999 Miata, 79,000 miles. The first time it happened was when
starting after being parked for about two hours. The engine ran very rough,
almost stalling, with the check engine light flashing. I checked the gas cap
and fuses but saw nothing wrong. After driving about a mile, the engine
suddenly started running normally, and the light went to solid. The next day
I went to the dealer, who checked the code and said I need new wires and
plugs. I had them do that, but the next day I had the same problem. This
time the dealer said it was the catalytic converter, which was still under
warranty. They changed that, but the problem recurred. The light then went
out by itself after I had parked the car for two days without driving. Since
then it's happened twice again. The dealer checked and said it showed the
same two codes (random misfire and cat converter). After checking with Mazda,
they now think it's the ignition coil pack, which is on order. Right now the
car runs OK (though there seems to be an exhaust rattling which I at first
thought might be the cat heat shield) and the check engine light is on solid.

A possible contributing factor is that back in October the car got partially
flooded - parked in an area that turned into a giant puddle, and ended up with
about an inch of water in the foot wells. It ran fine, though, and a
different dealer told me at the time that the water shouldn't cause any
problems (main concern was getting the carpet dried out properly) since all
the electronics are up high.

Any ideas about this?

Barry