I've done a search and have found no clear answer to this question.

I am very familiar with using Sims Surgery to clone and replace regular player sims and Townies. But I have heard that cloning over NPC's is a different matter because of their specialised clothing. I heard that you need to download a package of their clothing so it will be available in Bodyshop first. Is this true? I'd love some guidence before I take the plunge and try this.

some thing you can do is use the boolprop testingcheatsenabled true cheat then shift click on your sim and spawn "toms clothing rack" and choose dress like NPC and find the one you want!

Since you said you're familiar with SimPE to some degree....
Basically all you'd have to do, if you don't want them to show up in their regular work clothes
Go into the BEHAVs, Behaviour Function, "Funktion-Init" and prevent the Jump to line A (Put NPC Clothes on me)by setting TRUE and FALSE both to 2 in line 9 (this is only valid for MAXIs NPCs...for user-created NPCs just find the line where they change into their NPC clothes and prevent jumps to that line)
That way they would always show in whatever you put on them for CASUAL

if you just want to change their face you would't have to do anything after altering them in Sims Surgery
-le