What model? Any warning lights or buzzer? Was the CD bad? If it's a 90A, how is the link and sync, and how clean are the carbs? Is that 3000 limit only when running on the boat? If so, what prop are you running? When did the issue start?
Almost everything effects the RPM, so, you have to troubleshoot the engines three systems and determine, by process of elimination, what the problem is.
Start with the Factory service manual as a guide, and troubleshoot the fuel, electrical, and mechanical systems... in that order. No shortcuts on these.
