2002 Sportster Lt one engine runs fine other won't pass 3500 rpms

[Dellahan]

Rebuilt the 717 last summer broke it in ran fine topped around 7000 rpms. Put in this summer motor wont pass 3500 in the water. Take the boat out will do 7000 rpm on the trailer. Rebuilt the carb put new rectifier in checked the Jet pump for obstructions (none) same thing happens. Motor does seem to lag up to the 7000 on the trailer but not much? Was told to check the neutral switch this is a twin engine boat could this affect one engine and not the other? getting desperate any ideas.