At what point in the chocolate making process should I add things like nuts, herbs or spices, and how would this affect refining and tempering?"
I’ll try and keep this short and sweet.
The base answer to when to add additional ingredients is that it all depends what you want.
Nuts – I like them right at the end, while I am tempering. If you put them in while refining, you are going to have the associated oils to deal with, and while homemade nutella (hazelnut and chocolate) is great, the hazelnut oil inhibits tempering and if you use too much (40 % or so) it won’t even set up (since oils by definition are liquid at room temperature).
Herbs and spices – first off, if you are using herbs - Water! Be aware. You really need to use dried herbs or you run the risk of seizing your chocolate. But if you keep them mostly whole and don't release the water, you may be fine. Next. When? I personally like a smooth chocolate and like the herbs and spices added at the beginning of refining. Some people like the earthy texture of the herbs and spice and add them right at tempering time. Totally your call. Both will work.
As for tempering with chunky bits in there – it has the potential to make it more difficult. Lots of places for lower seed crystals to hide. You are probably going to want to hold at your working temperature (88-89 F for instance for Dark chocolate) for a little longer to make sure all the other seeds (1-4) are gone. And it’s helpful to get your additions (nuts mostly, but herbs and spices too) up to around the same temperature so you don’t plummet your chocolate temperature and wind up with a really hard to work with mass.
That’s about it. Add it either place to your liking. Be aware of added oils and water. Pay special attention to your temperature while tempering and take your time.
Nutted and herbed Holiday gift chocolates....what a great idea. Glad you thought of it.