People born without limbs do not seem to have the "missing limb" itch syndrome. (And those born with six fingers find it natural, too.) A simple hypothesis of the missing limb syndrome is just that one remembers the limb was there and what it felt like when the limb itched. It's like a dream in that the brain is activating circuits without necessarily having input.
But Doc, who or what is the "one" that remembers? The brain? Or its epiphenomenon (i.e., the mind)? If it's the former, then the brain is giving a false report about the current state of the system. If it's the latter, then how does the mind know more than the brain does, since (apparently) you define the mind as epiphenomenal, that is, as a by-product of brain activity?
Also, I think your statement implying that there is no "input" to dream activity may be incorrect. But that depends, I suppose, on whether it is true that the mind or consciousness has independent reality. For if one were to admit that the mind is an existent in its own right, then one could hypothesize that the inputs to the dream state were coming from subconscious levels of the mind.
BTW, nowhere have I suggested that by being an existent in its own right, the mind can get along without a brain. But just because synergistic relation exists, that doesn't necessarily mean the mind is an epiphenomenon of the brain.