If you own the car, do what you want to it and enjoy it while you have it. Like Robbie said, store the stock parts carefully so they don't rust or get damaged and if the day ever comes that you intend to sell the car you can spend a weekend replacing any bolt-ons back to stock. You can't enjoy living today if you're only worried about tomorrow.
As for buyer's perspective.. I sold two of my toy cars this year and while it took a long time to find buyers (both cars were highly modified, one a totally different late-model engine swap and build, the other essentially a street-legal drag car) but then they both ended up selling within 5 days of one another. Definitely have to wait for the right buyer. In today's online world, it also helps to get a lot of "tangible" data on the car available on the net. I put together a free page and wrote out all the mods and car data, then added detailed pictures of EVERYTHING (because they always want to see every nook and cranny), and then also loaded hosted free videos on YouTube which I linked to the free blog account. You can post your link in any car ad you post so buyers can go right there. In one sitting they have all the numbers, plenty of high-res photos, and in my case some nice audio to make them drool.
My perspective as a buyer looking for a used Viper would be... if it's modified, I want to see bolt-on only and low miles. This is more so that I know the internals haven't been played with by someone inexperienced, but also so I can quickly and easily change out any mods that I might not select myself. The low mileage part is just so the paint and interior condition are in generally better shape, because for all the buyer knows the car may have been driven one quarter mile at a time.
An oddity I have has to do with buying any car with aftermarket rims. I don't mind a Borla versus a Corsa catback, or Belanger versus Borla headers, etc... they will all perform within the same realm as one another. But rims are a highly subjective and personal touch on a car that will make or break a decision to buy. For me, anyway. But I'm picky.