I know this comes with a lot of mods already but when I go on Nexus even if it is just to update the exiting mods I get a incompatible message. I generally stick with Vortex but even if I manually try download I get the message when I try to unzip the file to install the mods into the mods folder I made. Is it hard coded in somehow that you can't manipulate the GOG version?

I don't know what exactly your issue is (you don't provide enough information), but "incompatible" means incompatible, not "can't manipulate". Your "DF GOG Cut" is based on an outdated version of Daggerfall Unity (DFU), and many mods contained in the GOG Cut have been updated to the most recent version of DFU, and at least some of them are now incompatible with the outdated GOG Cut version of DFU.

The GOG Cut is a package which hasn't been updated for a long time. Will GOG update it in the future? I don't know, but I doubt it. If you want to continue playing the GOG Cut, you're probably stuck with the version available from GOG. It's the risk of using packages like the GOG Cut.

PS: In theory, you could try to update DFU to the latest version manually, and then to update the mods manually. It may work, but there is no guarantee that mods not updated to the latest version of DFU continue to work, and that your savegames are compatible with the manually updated package.

Thank you for the reply. It agrees with what I was afraid of. It isn't a bad game as the GOG cut but definitely outdated as far as the modding scene.

General recommendation for DFU:
- Download and install Daggerfall (not the GOG Cut).
- Download, install and configure DFU.
- Select, download and install the mods you want (latest version), if you want to play mods. You may have to acivate and configure them in DFU.
- Play.

You could try to find out if your GOG Cut savegames work in your new installation. It will probably work, if you install the same mods which are contained in the GOG Cut (the store page has a list of the mods in the GOG Cut). Otherwise it depends on which GOG Cut mods yuo didn't install for the new game.
It may be better to start a new game than to install all the GOG Cut mods.

A general rule of thumb for using mods:
- Install only the mods you want. Inform yourself about (if there are any) mod bugs and conflicts between the mods you want to install.
- The fewer the better (reduces the risk of mod bugs and conflicts between mods).
Personally, I'd add another rule (for me it's rule #1, but I know that many players have a different opinion):
- At first play the game without mods (starting with classic DF without DFU). Only use mods to try to resolve issues you have (YOUR issues, not those of other people) with the unmodded game.

Is that what the DFU GOG Cut means then? That list of mods are what is in it? I was confused if that was included in the install or if it was just recommended mods.

The DF GOG Cut is a preconfigured bundle consisting of Daggerfall, DFU, and 30-odd DFU mods (listed on the GOG store page). The mods were selected based on subjective criteria (which means you may agree with them or not), and the mod creators were not always asked for their approval (to include the mods in the bundle).
You may want to read the article "Migrating Away From GOG Cut" on the DFU home page. Link:
https://www.dfworkshop.net/ (scroll down).