A muscle cars lack of originality, especially the engine, subtracts significant value. A muscle car just isn't a muscle car without the engine. Take two examples: a '70 SS396 and an '70 plain jane six cylinder. Say both cars are missing the original engine, and both now have a nice 350. The plain jane probably is worth more (more desirable). The SS396 will be worth considerably less; what is a SS396 without the 396? What if the muscle car doesn't have the original engine, but it has an identically built replacement? Some will say that this is good enough. Some won't.
In the restoration circle, anything modified or non-original hurts the value of the car. Generally speaking an original, unmolested Camaro is worth more than a modified one. If your prospective car is modified, ask yourself the following questions: Do I like the modifications? Are the parts added something that has value and can be sold? For restorers, how much will it cost to replace missing/damaged parts? And finally, since you may one day sell your beloved Camaro, will a future buyer like the modifications? If you are the modifier, hang onto all of the original parts that you take off no matter how seemingly small or insignificant.
Sunroofs and stereos--both are commonly encountered. These reduce the value of a car significantly since the parts hacked for installation are expensive to replace.