to alter settings you need the hp calibration kit did you get this when you purchased the bike? this is a separate purchase to the hp ecu, but fitting the ecu shouldnt cause any problems with the traction control.
this may sound obvious but check the following:
make sure wheel sensor rings are fitted and not damaged, make sure the front wheel is fitted the righ way (sensor ring should be on the left side) has the abs block been disconnected? this is under the seat near the battery, lastly and most obvious is the traction control swithched of using the switch on the left handlebar?
we use standard clutch plates with an stm slipper clutch, the stm allows for smoother race starts, never had any problem with the standard clutch plates