Here's how to start Pathway Tools from the command prompt in windows.
By default, Pathway Tools will install to C:\Program Files\PathwayTools.
It launches with a ptools.bat file in the install directory, so you should be able to
launch Pathway Tools with the python server with:
C:\Program Files\PathwayTools\ptools.bat -python
If this doesn't work, but your desktop shortcuts do work, try clicking right on the ptools-lisp
shortcut and select the properties tab. The command string the shortcut uses is displayed in that tab.
You should be able to just copy-paste the command string into a command prompt, replace -lisp with -python
and run the command. You probably don't need the empty-string ("") in the string either.
Let me know how this works, and remember that PythonCyc is currently still python 2.7-based.