Taking one step at a time. About this warning:
Warning: Connectivity configuration "Arduino connectivity config using serial" has already been registered. Check that there are not multiple sl_customization.m files on the MATLAB path that specify the same connectivity configuration name. , this custom registration is not loaded.
It looks like you may have more than one copy of the files on your MATLAB path. From the MATLAB command window, try
which -all arduino/sl_customization.m
to find out all the instances of this file on your path.