Usually there is, or isn't, spark. Are you certain there's enough fuel and cylinder compression is adequate?
I'm guessing yours has a single ignition coil, others used two separate ignition coils later on. In some cases the CDI unit does break down internally and spark voltage/current suffer as a result, this might cause a dual-coil to not fire on one cylinder or single coil to not fire at all but 1st you need to confirm there's enough fuel/compression.
I keep a squirt bottle of pre-mix fuel on my bench for this purpose, I don't like using either starting fluid b/c I've seen the damage it can do. A reliable compression gauge is your friend.
FWIW, Seadoo began integrating the CDI unit into the MPEM for Rotax motors circa 1998ish