You sure you have the ports cleaned out good. For a test open the valve w/ your fingers with the engine idling (be careful not to put a hole in the plastic diaphram). This should stall out the engine if you open it abruptly enough. If it doesn't almost stall the engine then you need to clean out the intake ports more.

No where for a p0401 does the flow charts take you to a section where you need to replace the ecu.

Also make sure you don't have p1491 set also cuz the helms manual says to check that out first. Those flows show ecu replacement.