Axiom: an engine is an integrated system. Thus, engine modifying ought to be done using a systems approach: when you change one part you must understand that it will affect other parts in the system.
DMH Motorsports recommends a supercharger under-drive pulley of 15%. The reason has nothing to do with the poly-V belt breaking but rather unfavorable issues caused by the increased supercharger RPM.
The 2800-3500 RPM lean flat spot while in cruise mode (manifold vacuum, light engine load, low RPM) seems to be a function of intake port shape, fuel injector location, and the resulting inability to carry fuel. It is noticeable when you try to accelerate: you open the butterfly and mush. From our experience the MINI is not unique to this phenomenon: it has been studied for 40+ years on cars as varied as sprint cars to Civics. ECU tuning can most definitely help but not totally eliminate it, BMW/MINI included. The only other known possible solutions are to redesign the intake ports and/or install a purpose built header such as the Stahl header; however, neither are guaranteed solutions.