hi,
as per the install documentation you need to disable the boost control kit.
you can disable it under ETC, FUNCTION select on the hand controller, this will clear the engine check light being on.
when the engine check light comes on, it will highlight the broken sensor in ETC, SENSOR SW CHECK and you will see BOST is highlighted, as you don't have the boost control kit, the boost senor returns no value, so the engine check light comes on and stays on
i have no idea about your aftermarket alarm led being on, but the PFC should function the same as the stock ECU in terms of the ECCS control and relays etc