Sounds like it may be the neutral safety switch, if the MPEM senses the gear lever is in the neutral position it sets the rev limiter to about 3500 rpms, it also must sense it in neutral to start the engines, so if your switch is sticking in the neutral position it may explain your problem.
Ike
p.s. these boats should always be ran with full synthetic low ash type API TC oil Do not use NMMA TC-W, TC-W2 or TC-W3 outboard motor oils or any oil sold as Ashless even if they also claim API TC