I've always believed in:
a. only making mods that can be "undone" in a day or week at most.
b. doing what makes you happy.
Life is too short to worry about keeping any car so "stock" that you can't enjoy it....although there is a lot to be said for the "excitement" of having something to show off that has a lot of historical value to it ( I like seeing those '55 Ford Station wagons at car shows with every detail exact as it was then--right down to the picnic basket and dealer brochure, too).
There aren't a lot of these cars left out there, and the "stock" look of individual CS cars does hold some interest and value--as opposed to a modified coupe with silmular parts. And we know that there are LOTS of those out there!
This was a promotional effort by Ford, like the Sprint package, it was the California version of that, using Shelby parts for the (Southern) California car culture.
I can relate to seeing a stock CS with those "dog dish" hubcaps, stock narrow whitewalls, and a single exhaust, perhaps in a color Shelby didn't use for that year. It's sometimes a conflict (from a car design aspect) of what the GT/CS (HCS) is supposed to look like: "a Shelby Coupe", or "a dressed up Mustang Coupe"? I'm not knocking the "stock" look, but to just say how in Ford's attempt to use the Shelby parts, that sometimes the performance look can work against the "stock" aspects of the Mustang, as it was sold then.
When you see that rear end, spoiler and taillights, etc, you'd expect some sort of "bad" looking big exhaust pipes coming out of there. After all, it was advertised to be "Inspired by the Shelby GT".
I support the idea of keeping the original rear valence, and going with the GT valance. Keeping any and all original parts replaced IS a great and well-thought out idea--especially for resale.
You have to decide if you're modifying your CS for an eventual resale-OR-for your own enjoyment--now? It's up to you. I'll support a total concours restoration for competition, and I'll support some simple mods to make it fun, too! It's all in what you want out of the car, and how it satisfies your interest.
I personally like using the "CS-Shelby" (logo) parts of that specific time period (March-Sept., 1968); like valve covers, intakes, etc. as outlined in my book. That way, it adds to the interest, and makes it more of a "it was available then" interest at car shows. It's like seeing those "Frontenac", aluminum intakes mounted on the top of Model A four-bangers. Kinda exotic.
I wouldn't worry too much about keeping things TOO stock to enjoy it; although I can also appreciate preserving the historical details of these increasingly rare limited-edition Mustangs.
It's up to you.
Paul.