A bunch of people helped me get it working. I made a video tutorial to simplify the process, and uploaded a single .7z file with everything you need to get the best texture sets working.
http://www.mediafire.com/?91y53bjjkuzrkw4. Here's the link to the video tutorial:
http://www.youtube.com/watch?v=gBwj8TcGuS8
Install these:
Windows .NET Framework:
http://bit.ly/dzMnWE
Steam:
http://bit.ly/1Wkh2s
Your latest video card drivers with Steam
Star Wars Jedi Knight: Dark Forces II from Steam
The .7z contains these, so you can ignore the links and do what the instructions say.
Get smackw32.dll:
http://bit.ly/fZfwEd -> your main jedi knight folder
Get jkpatch:
http://bit.ly/hkbhwy -> main jedi knight folder
Get Jedi Knight Enhanced:
http://bit.ly/hCo88A
Get Jedi Knight Retexture:
http://bit.ly/ebQHBm
Create a folder called "Mod"
Drop JKE.gob and JKR.gob into Mod
RMB JK.exe-> Properties -> Compatibility. Check Disable visual themes and check Disable desktop composition. Click Apply. RMB JK.exe -> Create shortcut.
RMB JK.exe - Shortcut -> Properties. At the end of the Target line, type in "-windowgui -path Mod" Click Apply.
Double-click JK.exe - Shortcut to start the game. Go to Players -> Single Player. Create a profile. After the game starts, hit Esc -> Setup -> Display. Check Enable 3D Acceleration. Check Backbuffer in System Memory. Set 3D Accelerator min texture size to 1. Select your screen resolution and bit depth.
If you have a save game you want to continue, then you will have to end the level first to get the textures working. Hit the t key -> type in thereisnotry and hit Enter.