I switched from a 225 Etec to a new 250 Etec last year. For some reason with the same prop I lost 6 mph out of the gate. The 225 was a 60 degree motor and the 250 is a 90 degree motor. Do you think this is because the motor is not broke in yet?
Are you running the same RPM with the same prop, the new motor may now be under-propped? Also, as far as break-in, there may be a timed limiter programmed into the ECM as BRP/CanAM/Bombardier typically does with their products, especially with the ETEC. Have you referred to your owners manual, or called the dealer?
Is your max RPM still correct? It may be that the new motor has a different drive ratio, and therefore requires a different prop pitch to accomplish the same thing. Using the same props, you may be either over-propped (lugging the motor) or under-propped (hitting the rev limiter).