IMO the rules of thumb are pretty simple;
Understand that any modifications you do to a rare or desirable original car could (likely) devalue the car to some degree. In other words, don't expect that others will agree with your personal modification tastes/preferences come selling time. Generally speaking the amount of value difference will be equal or slightly greater than the cost of reversing the modification (if reversable at all). Also keep in mind that regardless of what the custom parts or work you have done costs, it is 100% valueless to a guy who'd rather have stock componants in thier place, this is money you'll spend that you'll unlikely ever see again.
So, IMO, do anything you want to your car, after all it's your car. Just don't get upset when you can't get what you want when it comes time to sell it because in all likelyhood, you won't.
To each his own, if they were all stock (my personal preference) things around the Mopar hobby would be pretty boring