I have a 88 35th Anniversary car, which I believe to have original paint with only 32K miles, but the headlight covers seem a different shade than the rest of the hood/car. Is that normal?

Certainly possible. The bumper covers can also sometimes be a little bit different shade. It's due to the difference in the base materials used on the different parts being painted. The yellow cars were really bad about paint color differences between the parts, as was the golds...which is why gold cars are pretty rare, in comparison.

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Quality Control was not at it's best for the C4s (although better than C3s). So it is certainly possible it came from the factory that way.  However, unless you are the original owner of the car (which obviously you are not) it is hard to know if the hood or headlights or anything has ever been repainted.