Don't use the .exe that it comes with, it will crash.
All you have to do is drop a copy of EDuke32 into the data folder click and on eduke32.exe. It's as simple as that. All the cons, art, build tables etc. are already in the data folder. The other folders are just for the front end he used.
This is a very pretty game:
With some polishing and some code work, it could really be something special. I only spent a few minutes with it, partially because of the "invisible font" bug that makes it impossible to change any settings. I don't really want to play it, but I think I will use god mode and walk through the maps just to look at them.
From what I saw, the overall art design and build quality looked very high. It was very pleasing to look at. However, the one enemy I saw (a goat man) looked and moved like crap. The NPCs were much better (but of course they weren't animating). The crossbow was kind of cool (the one weapon I saw besides the fists) but you could see the bottom of the sprite when you walk.
It's too bad that the game was hobbled by using outdated JFDuke with the very limited scripting ability, crashing on Vista etc.