All the original files can still be found on
https://allfearthesentinel.com/ under "WADs" by searching "woc" as the keyword. That includes all the files on this thread:
viewtopic.php?t=35846 which are v3a main, nothexen patch, heretic patch, doom patch, strife patch, moc patch all under their original file names. A user kindly reuploaded the lite version on page 70 of that thread, as well. Also includes the mysterious 3.1.4 update which fixed bugs and made changes to things such as poison damage dealing over time. You just have to make sure to download and run the right files.
Since I brought the mod back into light and was asked about addons, just going to give a quick shoutout to most of the content I know of that currently uses Wrath of Cronos as a base:
Hexen: Cult of Despair =>
viewtopic.php?t=65993 (Great campaign, beautiful maps.)
Diablo 3D =>
viewtopic.php?t=59198 (Basically Diablo in the doom engine, the base system this addon is from. Atmospheric, and really feels like you're playing the Diablo games in first person. Also brings over monster damage type resistances and immunities and such.)
Hexen: Land of the Serpent Riders =>
https://www.doomworld.com/forum/topic/1 ... -complete/ (Custom campaign for zandronum; won't work with my addon since it uses zscript but last time I played it was an amazing experience.)
ElPoder's Unofficial "Hard" Wrath of Cronos
https://www.moddb.com/mods/wrath-of-cro ... al-version (Wrath of Cronos but with a ton of mechanical changes. Last time I checked this adds skill cooldowns and a ton of other things to make the mod harder. Might not be everyone's cup of tea for those looking for a more casual original experience but appreciate their work nonetheless.)
The other files that I can think of that are being hosted are from the original doom monster replacer, which has received a ton of fixes and patches and additions. I believe all the stuff on the replacer in itself is up to like 7 different files last time I checked. I also made a quick mock-up of this addon for use on Zandronum using those specific monsters but it's a little rough; might upload that as well if I get to fixing it. For posterity's sake, I decided to run this with Doom, Heretic, Hexen, and Strife, and I've had drops with no issues so far with this little minimod. Drops right now are meant to be rare but they're insanely scarce; might boost it up a little if I feel like it needs it. Code probably isn't the cleanest, but it works.
EDIT: I updated the main post with another addon I decided to make, which replaces the default cleric shield and sounds with the one from the Heretic + Hexen re-release. With that in mind, I decided to consolidate anything I make into a single post and changed the title to reflect that.