Do you have MSD on the engine?

rotor?
 

That reminds me of the old GM HEI rotor proublem where the spark would burn a hole through the rotor button and start missing a cylinder. You would see a brown spec on the rotor that was a burn hole. It could be the bad plug wire caused the new rotor to fail.

I'll double check the rotor, and no MSD. I swapped valve springs but creased the exhaust manifold gasket, so I can't fire it up until I get antoher gasket today. Thanks for the suggestions guys!

you also need to check the height of the valve when its closed,could also be a mushroomed intake valves

It sounds like your ruling out the common stuff.
It's a long shot. But the 2 cylinders that are misfiring are opposite in firing order. Have you checked the distributor rotor that triggers the sensor. Could it be loose, bent, or damaged?
Gary

I was thinking that very thing, the 2 cylinders are each exactly 3 apart. Tonight when I put on the manifold I'll check under the cap. I haven't yet because both cap and rotor are new, but this problem is out of the ordinary, so I won't rule out faulty new parts. Thanks, I'll keep you posted.

Offshore addiction, would mushroomed valves pass compression and leak down tests? I've never encountered that condition.

Everything is back together now and I rechecked the ignition components, still not finding a problem there. Tomorrow I'll fire it up and we'll see if the skip follows the springs to #1 cylinder.
Although I think I'll find a nice solution at the Lauderdale boat show in a couple of weeks!!:p

yes,they actually stay seated,the stem just sucks up into the head farther and the outer part of the valve still stays seated,theyll make the motor act like you have a bad cam,or a weak valve spring,very common on stock type motors,theyll actually make the miss come and go,you said that your motor got a little warm,that may have got the valves hot in the cylinders,probally while you were on plane under load.in fact theyll accually show real good compression because ther not opening far enough,if the valves installed height becomes taller,the valve springs installed height becomes weaker,hence your messing with the valve springs.....youll never find it unless you can spot the height problem,or you yank the head......remember you have hydraulic lifters which can accually stay pumped up instead of deflating......making your cam lobe measurement stay very close to perfect.

Just to be clear, the rotor I was referring to was not the one right under the cap. If you remove that rotor you'll see the one that triggers the sensor.
Good luck.
Gary