It's actually quite simple once you wrap your head around the instructions. I almost gave up on it the first time when I couldn't get it to work, but perseverance saw me through.
You need to run the whole thing through a command prompt (if you're using windows: Start>Run>command). Navigate to where you have makephn.tcl stored, then to run it just type in "makephn.tcl phnlist.txt" where phnlist.txt is the list of wavs and text files that you want to convert. Just remember that for it to work your wavs need to be mono, and you need to have a text file of the dialogue being spoken in the wav.
That will generate .phn files, which you'll need to convert to .lip files with the lip synch editor.
If you need more specific instructions you can catch me on MSN. It'll be easier to explain one on one.