i think you have to seriously ask your self "are you ever going to sell it?"
If you are, like said, keep to period correct mods out of the catalouge or pure concorse condition.
If not, do what you want, its your car.
I never plan to sell my car, so im modifying it the way i want (not that a 260 is worth more that a 240, even though less of the 2 seaters made it into the country)
As for putting flares on it, if you want to do it, then go for gold.
Skins can allways be replaced, and if you dont want to cut the rear guards, you can allways leave it jacked up a bit and adjust the bumpstops so it wont bottom out.
screw holes in a guard are very easy to weld over and make a seamless repair.