Check engine light flashing only over 5500-6000 rpm

[2door2nv]

Hi everyone. I have a 2000 Porsche Boxster 5 spd and just replaced the engine with a used very low mileage engine. I replaced the the flywheel, clutch and most of the parts from the new engine were installed. The problem I'm having is that when the car goes over 55-6000 rpm the check engine light starts to flash, then I let off the gas and it flashes for a bit then goes away. This problem was happening with the old motor as well. The only thing that was salvaged from the old engine were a few hoses and wiring harness because the new engine wouldn't match up with the ECU. Anyone know what's causing this to happen? Thanks.