The Mugen ECU is a static map. You are better off to buy something that will allow you to tune the car to the changes you make. YOu can get a power FC and datalogit for $900 or so (No need for the commander unit) or you can get a Hondata (Not sure what cost woudl be since it depends on features).

Both will out perform the Mugen ECU and cost less. VAFC is an option but nothing like a full stand alone like the Hondata or PFC.