2009 RZ2 pulsing

[Powerlock25]

Boat runs fine at idle
at 2000-3500 rpm boat pulses...feels like it loses power (RPM dips briefly and then Returns)
pulsing is felt by everyone on the boat

backstory-
the problems were much worse - pulsing at low RPM’s as well...engine died twice this summer and Almost wasn’t able to idle in
mechanic recommended I replace cap and rotor (but also sold me the fcc filter and inline filter I called for)
that helped a lot...ran perfectly for a few outings...now the pulsing is back just not as bad (however wouldnt want to pull a skier)
I replaced filter in the water separator
didnt seem to make a difference

I plan to replace the inline fuel filter but don’t know where it is
any other recommendations? Spark plugs?

[chpthril]

I would certainly replace plugs and wires. Then check fuel pressure.

[boatwakes]

Whats them there dang ole engine you got in that thing? Some of the booster pump failures act as such and other times it's the anti siphon valve at the fuel tank. Like Mike said, throw a fuel pressure gauge on it and report back.