Beware of extension cords in series with the power to the Base if you have any excess wire coiled up. The coiled wire can form a "choke" that will lessen the (beneficial) TMCC/Legacy signal that gets into the house wiring.
I suggest the first thing that you try is to unplug the wallwart power supply for the Base and run the engine in conventional mode. Is there any slowing at the troublesome points? (This assumes that you can operate conventionally....)