@FoShizNat - yep no prob lets try and figure out what going on.
First if you haven't already... maybe in your options under the HUD Information section turn on the checkbox to display icons over resources in the strategic view (the checkbox next to the pickaxe). That will show a red padlock or a orange pickaxe over Resources depending on whether you have the technology that allows use of a particular resource. It just makes it a bit easier to spot resources on the strategic map, because the red padlock really stands out.
When you're generating random maps to test this... try Medium size, everything on the default setting, and 4 opponents. That should be enough to give you all resources.
The 4 custom resources in this mod are set to have 0.5 per player for each resource. So if you have 4 players there should be 2 of each resource. Clay Pits are not based on number of players but are fairly common (as you suggested) and you should get at least one pretty much every time on a medium map with default settings. I'd expect at least 4 as a guess.
Enable cheats so you can uncover the map. Sounds like you've already done that.
Can you confirm that you have copied the file JB_CustomShardsNewBooks_Core.xml from the install zip to the CORE -> data -> English directory as per the install instructions ?
1) Extract all the folders to your LegendaryHeroes Mods folder, normally Documents/My Games/LegendaryHeroes/Mods
2) Locate the file “JB_CustomShardsNewBooks_Core.xml” (should be in Documents/My Games/LegendaryHeroes/Mods/Demons and Wizards) and move it to your Legendary Heroes\data\English folder... this folder location will be something like C:\Program Files (x86)\Steam\steamapps\common\FE Legendary Heroes\data\English depending on where you have your steam game files located.
3) Make sure that you turn on "Use Mods" in the in-game Options menu
If you've done all that and you can't see any of the 4 new resources, try downloading this file:
Drop it into CORE -> data -> English, overwriting the file that came in the mod zip. This debug version changes the CLOTH MAP icon for the 4 new resources to a yellow question mark icon. It makes the new resources very obvious on the cloth map.
Save that file, generate a new map, use Ctrl-U to reveal the map then zoom out to cloth mode and look around. There should be 8 yellow question marks on the map if you chose 4 players.
If they're not there then something is really wrong.
The other thing for you to test.... have you turned off Mods and checked to see if the Clay Pits are appearing ok on random maps?
Let me know how you go with this.