The firing order... looking at the front (from the transom) of the engine is:
1 2
3 4
5 6
Now.... if it happens to be numbers, 1 and 4... then you have a bad trigger.
If it's 1,2, and 3... then you have a bad diode in 4, 5 or 6. (they balance each other, for charging)
If it's truly only 1 and 2... then you either have a bad wire some where... or both coils/CDI's are going bad. (They don't have a common part that would kill those 2, without causing a problem on another coil)
Somewhere above... I asked for a picture of your engine. I kind of need it, to know exactly what engine we are dealing with. It has changed over the years. Right now, I'm assuming it's an early 240 EFI. Also, I know some people have come here saying they have one engine... and when we get a pic, it's something else. FYI... there are basically 5 Merc engines that Seadoo used, and the ignition is different on all of them.
210 carb
240 EFI early
240 EFI late
200 DFi (optimax)
250 DFi (optimax)