It's explained, more or less, in Stranger Souls, and it's tied to his being a director of Aztechnology. That connection is likely why he is also no longer a director of Aztechnology.
As Wak said, they can't just swap brains because his brain is a matrix of cells within the vat. A clean body would have the same disease, maybe, but so what? CFD suggests that consciousness and memories/personalities can be transferred electronically via nanotech, but again, so what? Every digital upload is merely an impression of the person—a
persona—and not his or her actual self. The single exception is Quicksilver in
Imago. There could be an army of Roxy clones with the disease removed and his biological memories, personality, etc. implanted. However, none of them are Roxy because none of them has, as DeathStrobe noted, what Shadowrun refers to as his Essence.
Why Roxy hasn't availed himself of the resources and opportunities since Crash 2.0 is the billion nuyen question.