Now the mod has an optional part. See the description.

If I understand correctly, you copied all three mods into one CUSTOM folder. But this is wrong, each mod should be in its own folder of the corresponding game.

They aren't so much enabled, rather installed. I should have clarified I'm using MMod with the universal custom folder fix. As I understood your instructions, all packs needed to be installed because each game uses the same textures. So I have all 3 of the packs in my custom folder. I noticed if each pack was in each game's own separate folder, they wouldn't work.

Hello. Did I understand correctly that several of my mods were enabled simultaneously during the game? Because, as I already indicated in the mod description, that during the game, for example, in EP1, the other 2 mods for HL2 and EP2 should be disabled. Check this, please. To be absolutely sure, it is also better to disable any other mods for the time of checking. If the problem remains, your saves will help me a lot to fix these bugs.

Here's some pics:
https://imgur.com/a/VpYTbHu

So I've been using your texture packs for a playthrough of HL2 and the episodes and they've been a great upgrade to quality. Great Job. Then I get to EP2 and the Vortigaunts are invisible except for their eyes. In the console, I see the error "Failed load of .VVD data for vollion_guard.mdl". Reason I'm commenting on the pack for EP1 is because with some testing, that seems to be the culprit. I removed EP2 pack and he was still invisible. Removed EP1 pack and he was visible again. Put EP2 pack back and he's still visible. So something in the EP1 pack is causing the Vorts to be invisible only in EP2. Any idea what might be causing this?
As an aside while I'm here, HL2 pack seems to be causing weird textures for the grass in EP2 as well. Same testing confirmed HL2 was the culprit.