I have used both exhaust systems and have had very good luck. I have used the EMI Exhaust on a 454 mag and 454 mag mpi.
On the 454 Mag the increases were minimal (@2mph), until I made considerable engine modifications.
With the 454 Mag MPI, I included an ECU upgrade kit from Arizona speed and Marine. With some prop work (lab and 1 inch pitch increase), I saw a solid 4 mph gain on a Velocity 260. Still needed to run RPM @ 5200-5300.
Have had 3-4 MPH increase with CMI on 496 HO on a Velocity 290. Just received the Whipple reprogram back. Will be testing with that this weekend.