So I'm trying to get my custom guard to wear some clothes that I've downloaded, so I load the master file and the clothes.esp and then mymod.esp and set mymod as active file, fix my NPC and give him the right inventory, the preview works, also when I've placed the NPC I can see the clothes, but not in-game. Help?

I am new to mods, but I just solved the same problem (I am stuck in the next step … see my question just before yours)

Try the following: (if it doesn’t work, I guess you will have to wait for a more experienced modder to answer)
1. Duplicate the item(s) you want to use from other mods

• >> CS >> Object Window >> Double click the item you want to use
• >> change the item’s ID to something of your liking
• >> click OK
• >> Answer YES to the question “Create a new item” (warning: answering NO will change the original item and that may be a problem if others use your mod)

This will create a new item for your mod and it will immediately appear in the Object Window list

2. Use this new item to equip your NPC, instead of the original item

If you are planning to share your mod, there are some other things you will have to take care of. But I can’t help you here, as I am finishing my first mod and didn’t get to that stage yet.

Npcs seems to be protection Oriented or just vanity... They will wear the most protective gear or the less cheap one, most of times..
A time ago I had a problem in making my NPC wearing some leveled armor, this was easily solved putting anything vanilla, cheap and/or low armor in its inventory. Maybe this occurs with customized items too, not sure.

They seems to need some vanilla reference to trigger the choices.

Edit: the NPC cited above appeared naked even when her inventory had the leveled armors, giving her a cheap fur boot was enough to incentive her to wear the correct ones.

Edit 2: I'm supposing you have all ESPs active in game, of course.

Works like a charm thanks