Yes, I placed it all in the c:/ drive

The full tree download is just the installation folder for D2:LoD after Ensley installed D2SE and HUv1.6.

It's recommended that you extract that folder to C:\D2\, so that you'd have the this kind of folder tree:
C:\D2\D2SE.exe
C:\D2\Game.exe (along with about 60 other files and folders)
...
C:\D2\d2xmusic.mpq (along with another 10 or so .mpq files)
...
C:\D2\MODS\HUv1.6\

Once that is done, you'd need to change the permissions for some of the .exe programs so your computer will run them as if they were an administrator (just like they used to back in 1997), so you'd right-click on
D2SE.exe
Game.exe
Diablo2.exe
maybe D2VidTst.exe (it's configured on my machine at least, but it probably doesn't need it)
and configure them to run as if they were on WindowsXP, and as Administrator.

Before working with HUv1.21, run D2SE.exe and confirm that it opens a window such as (I just grabbed this pic from the internet):

Top Right
StartPlugin - Runs the mod selected on the left (you could also just double click that mod's banner)
StartD2 - Starts D2 and I think ignores mod files. Generally not what we want.
Display Options: my machine works well with DirectDraw, but if the game seems slow or strange, then try Glide. You'll need to configure Glide (it'll open another window where every setting has some information at the bottom to give you a hint about how to set it. Most players swear that Glide is the way for them, but I don't have too much experience with that.

Middle Right:
Checkboxes to Disable Sound, allow HC chars even though you might not have completed SC Normal difficulty, use the PlugY mod (I don't know everything it does, but it allows your SinglePlayer chars to share a stash, and lets the stash have many pages of items. Some mods can't work with this, I've heard that HU can run with it. I don't know how to set it up, but there are online tutorials).

Bottom Right:
D2 Startup Commands: these two checkboxes tell D2SE to tell D2 to look for a "data" folder (e.g. C:\D2\MODS\HUv1.6\data\) which could contain overrides for all the data in file patch_d2.mpq. You might use this if you downloaded a no-extra-music version of HU but changed your mind and wanted to grab that music from another version (e.g. one guy did this recently).

Try running a vanilla version for a minute, just to see if you can make a char and it loads. This would confirm that D2SE is not a problem.

Try running HUv1.6 for a minute (you might need to scroll down the list on the left), just to see if you can make a char and it loads. This would confirm that HU isn't a problem.

Let me know when you've gotten this far and if you need a hand putting HUv1.21 into the MODS folder.

okay ill give this a try thanks for the consistent responses!

Well wait how should my files look? Should the 1.16 files overwrite the original D2 files after installing it?

If you're using Ensley03's file tree, then you shouldn't have to worry about installation, everything needed is in the folder, but you might have to edit permissions on some of the important files like Game.exe, DiabloII.exe, and D2SE.exe. Please read the information in that thread if you're still not sure how that works, otherwise you might accidentally be making this harder than it needs to be

Okay so I did all that got the game up and running however now when I'm playing in 1.16 the weapon equip area is all wonky. How can I downgrade it to 1.21? just create a folder in the mods section?

That's right, make a new folder with a descriptive name, like HUv1.21, and then decompress the files from HUv1.21 to that folder. You'll need to include the D2SE.ini for HUv1.21 file. That ini file tells D2SE what modsystem is being used and what .dll files to include, so it's a pretty critical file.

You don't have to delete the HUv1.6 folder, it might even be handy if you want to compare with your v1.21 folder and figure out what's missing if things don't work out well. There's a good chance that v1.6 folder was using the HighRes (1024x768 rather than normal 800x600) version, so it will have an extra file or two. That resolution mismatch is probably why things weren't aligned as you mentioned.

holy shit I think that fixed it! I went to graveyard and no issues! oh man I have really thank you, you were really patience and good with responses! Thank you so much for helping me out with this!

Good stuff, glad to hear things are cooperating. If you get tired of HUv1.21, there are also HUv1.3 to HUv1.7 available. If you wanted all of them available at the same time, then with D2SE that would only require about a gigabyte of hard drive space. I think it's fun to see how the mod has changed or changed back.