I have a set of Mercury 496 inboards with 1000 hours of troublefree operation. One is now not starting on first or second attempt and when it does start idles fine but under load developes a miss at 2000 RPM. I changed plugs and same result. I put an old plug in a plug wire and watched while cranking on it and when cranking and not starting I have no spark indicating it is an electrical issue. If I try again a few times eventually I will get spark and it will run.
Any ideas?

Maybe a bad coil pack ??

Tonight I traded out the ignition module and 4 relays on top of the engine from one engine to the other and it didn't make any difference. I did notice that when I was cranking the engine over when it was not starting once in a while I would hear a beep coming from the electronic tach unit on the dash and then it would start.

Beep is not coming from the tach. It's the alarm (possibly false).

You might want to try hooking up a timing light to each plug wire and try cranking it and watch the light to see if you are getting about the same spark time frame out of all of them. Also if you can try running the engine at night and look the engine over well for sparks going to ground from each of the coils and wires all the way down to the spark plugs them self. Look under the coils too, You might get lucky. Check and clean any and all ground and power wires and cabels to engine and batt.

I had, at least what sounds to be, a similar problem. 496 HO's that would develop a hic up, almost like a misfire. Our issue turned out to be some debris in the fuel lines. Go figure....

Not the exact same symptoms, but you might want to at least think about it

If you are getting a beep from the alarm at the helm, most likely you have a trouble code registering and with a scan tool that should indicate possibly whats acting up. The missing at 2000 rpms is probably the engine in guardian mode which will sound and act like a bad miss because the ECM is dropping cylinders to reduce power while in guardian mode.
If you boat in salt water, you can try removing all the sensor plugs one at a time, cleaning any moisture or corrosion out with WD-40 etc and replug them and try that for a simple test. Some times a loose or bad connection at an engine sensor on the 496 can cause this condtion.
I would suggest getting a scan tool from Rinda or getting the boat to a shop with one or borrow one and not take the time guessing and chassing your tail here.
Its nice to hear your 496's have 1000 hours on them.

Best Regards,
Ray @ Raylar Engine

Thank you all for the suggestions. I figured out the starting problem was the ignition switch. I found that while cranking I did not have 12 volts on the ignition side of the switch but I did when it was in the on position. Changed the switch and the starting problem went away. I have not had it out to see how it runs under load and it will be 10 days before I can try that.