You said I can react the copper quantitatively; is that mean not all the copper but most of the copper will react? As per your prediction, how much of the copper will be left behind?
No, that means over time, all of it does, and the soluble portion is valid for quantitative analysis for copper.
Regarding the Ag and Au, I think Ag is more reactive to HCl compare to Au
Really? Pure solid silver is going to react with hydrochloric acid, to produce solid, insoluble silver chloride, which will shield the mass from further action.
This is a common beginners problem with quantitative ore analysis. The beginner attitude of "I'm just going to soak it all in aqua regia, the strongest acid of all, and all that I want will dissolve." doesn't always work. Conc. nitric doesn't always work -- it may passivate ferrous alloys, blocking further reactions. Hydrochloric may form an insoluble crust with silver, lead, and mercury, even as other reagents reduce them to free metals. Since aqua regia is both, either or both effects (or perhaps neither -- like I said it may work) may occur. Your ore sample may require pre-digestion with hydrofluoric acid to dissolve enough of the rocky matrix, even though hydrofluoric is a weak proton donor. You should be able to read up on these particular topics in ore processing for quantitative analysis and the need for these procedures.
There are other metallurgical manipulations for you to review, cupelation is still practiced, electro-refining has been mentioned before in this tread. As has cyanidation, and I threw in bioleaching just for the fun of it.