Usually, changing the color will affect the resale value of the car but if a color change is done thoroughly and completely (door Jambs, firewall, etc) and to a fairly high standard, the effect will be lessened. I believe what will affect the value more is modifications depending on how severe they are. Lowering a car is a big turnoff to a lot of people and messes up the suspension geometry in these cars, stressing all the components such as the bushings and alignment becomes an issue in extreme cases. Modifications that are fairly easy to reverse will affect the decline in value much less.
It you plan to keep the car a long time, I would just do it the way it pleases you. But if you plan to keep it for a relatively short while, then the more you do to it to vary it from stock will hurt the resale price. Usually, few people like the mods other people do to their cars, so it makes it harder to sell at a good price.
