There are a handful of Oncidium crosses and species that I know of, that can have those black spots on leaves and p-bulbs. Onc. Sharry Baby is a common cross that exhibits these spots - every Sharry Baby I've ever grown or seen has had them. The spots are harmless, and are simply a trait passed on in breeding. As long as the spots you're seeing aren't obviously sunken or raised (which is a possible sign of bacterial rot or other infection), I wouldn't worry about them.
The p-bulbs being shriveled is likely a watering issue - either the potting mix has been kept too dry (yup, even sphagnum can be kept too dry), or the roots have rotted due to over watering. All of my orchids' p-bulbs tend to be less plump after a month or so, than they were at the store or greenhouse, and that's just because my environment is drier (low humidity and fast-drying mix). I'd say lift the orchid out of its pot and take a look at the roots. If they look healthy, then it's likely just been under watered. If they're all dry and hollow, then they're no good, and you'll need to nurse your plant back to health.
In the case that the roots are bad, you can let the flowering finish (which it sounds like is already happening), or cut the inflorescence off and begin nursing your plant to health. Keep in mind that producing and maintaining flowers is energy intensive, so if the roots are bad, I'd be inclined to cut the inflorescence and start rehabilitation.
Sorry for the long winded reply; I like to be thorough and cover all the bases. I hope this eases your mind, or at least answers your questions. Happy growing!
-Tim
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