If it helps anyone, here's a brief guide on how to convert a q3 map's .pk3 to .map. (You'll need the .map format for the Q3ToReflex program to work.)
Unzip the .pk3 and search for the map's .bsp. It is typically in the /maps/ folder within the .pk3. Save the .bsp somewhere (doesn't matter where).
Use NetRadiant (http://ingar.intranifty.net/gtkradiant/installation.html) to convert the .bsp to .map. You can do this by opening NetRadiant, go to File --> Import, and select the .bsp. Your NetRadiant window might give you an error (about textures or entities) but you can ignore this. It will also likely freeze for a moment while it decompiles the .bsp. Once the map has load (you will probably see a lot of caulk, pink and black checkerboard pattern), go to File --> Save As and save the map as a .map inside the same folder as Q3ToReflex.exe.
Now you should have a .map version of the map you want to port. Simply follow the steps for the Q3ToReflex. (Open commandline prompt, navigate to the Q3ToReflex folder, and then use the appropriate commands per the readme.)