For full details on MouseTool, and the official download, see the official MouseTool page. You must download the official version because this version comes only as a .EXE file.
changes.txt explains the changes.
The binary distribution 175K (EXE only)
The source distribution 512K (VC++6 project supplied)
Ensure MouseTool is not running, then unzip the binary distribution over your existing MouseTool EXE.
Now restart MouseTool. The About box should now say version 3.16.
I've discussed these changes with the original author, and he gave his seal of approval to an earlier (read: not as good) edition of these changes. I have not been able to contact him since. Eventually, I hope there will be a new official version of MouseTool with these changes.