If the decal sheet has yellowed set it on a window for a day or two to reverse this process. Yes they can be clear coated just remember they will need to be cut close to the markings to 'free' them from the layer of clear. Take a decal off sheet in question and try first to see results.
AM decals? The round marking could be sprayed through a round mask, yes there is AM decals & PE. Try Squadron mail order search feature thingy.
If the kit is still in plastic why not E-bay it & buy a modern kit of the Zero? You may be surprised what a vintage kit will fetch from a collector.