The menu is in /home/tc/.wmx
One way to change the menu is:
Copy .wmx to another directory.
For example, lets use /home/tc/.mymenu.
So you have a copy of the menu in /home/tc/.mymenu/.wmx
In /home/tc/.mymenu/.wmx delete System Tools, or make any other changes.
Add the following to /opt/bootlocal.sh
mv /home/tc/.wmx /home/tc/.wmx_old
cp -r /home/tc/.mymenu/.wmx /home/tc/.wmx
When you start the computer, you should have the menu as you set it up in /home/tc/.mymenu/.wmx.
Keep in mind, if you install additional apps, or make changes to On Boot or On Demand, you need to set up the menu again.
To remove it properly, you can do a remaster.