The ability to change port names of an S-Function from within a Level-2 MATLAB File S-Function is not available in Simulink.
The workaround is to mask the block in order to create your custom input and output port names. I have attached an example with this e-mail that shows a masked subsystem with port labels that were created with the PORT_LABEL command.
In order to set up something similar with your S-Function block, please do the following:
1. Select the S-Function block and all the signal lines going in and leaving the block.
2. Right-click the block and select "Create Subsystem" from the context menu.
3. Right-click the subsystem block and select "Create Mask" from the context menu. The Mask Editor window will pop up.
4. In the "Icon & Ports" tab, under "Icon Drawing commands", you can write PORT_LABEL commands as shown in the following document:
5. To make further edits, you can right-click the Subsystem block and select "Edit Mask" from the context menu.
You can also consider creating the mask programmatically, by following the steps detailed in the documentation:
