Just my opinion but yes, return it to stock and sell the farkles separately.
The farkles have value but not to everyone, and some farkles would actually reduce the interest of some buyers. For my own part, I avoid aftermarket exhausts as I find them loud relative to the stock exhaust. So looking at used bikes, not only does an aftermarket exhaust not add value, it detracts from the bike's desirability. And the same with saddles, windshields, ect.; if they are the very brand and type a person is looking for, that is great but if not, then they actually make the bike less desirable and frankly, worth less money.
Perhaps try selling the bike as a package, and if it does not go, take off the farkles, return it to stock or at least closer to stock, and reduce the bike's price by the amount you expect to be able to sell the farkles for (or maybe not quite that much, it would be great if you could get a few dollars for your labor).
Again, just my personal opinion.
Brian
Where is the best place to sell a Concours ? Should I strip it and sell it stock?