Sorry to neglect your question. I intended to write something initially and then didn't get around to it. I can think of two brain diseases off the top of my head that spare various brain structures that might be thought to implement and store "the self". This suggests that you at least need to do a case by case analysis?

A probably self-sparing disease is Encephalitis_lethargica which causes (or caused?) physical catatonia (probably by damaging some components of the brain that use or produce dopamine) while seeming to spare other things for long periods of time, such that they can be temporarily "mentally recovered" by the administration of L-DOPA even decades after the onset of catatonia. This was done experimentally in the 1960's and is reasonably accurately documented in vivid form by "Awakenings", a doctor's memoir turned into a Williams/DeNiro film). The symptoms are similar to Parkinson's which, from what I understand, can also sometimes be temporarily treated to "bring the person back for a while" using things like stem cell treatments.

The second thing I can think of that potentially "spares the person's soul" is amyotrophic lateral sclerosis. This is what Hal Finney and Stephen Hawking. Hal Finney has been signed up with Alcor for decades and announced being diagnosed with the disease here on LW in 2009, in his essay Dying Outside.

In contrast, trying to think of a disease off the top of my head that probably doesn't spare the soul, I would expect CJD to take out everything. My understanding is that it basically involved exponentially progressing conversion of "nearly all brain matter" into misfolded protein that catalyzes misfolding of protein that catalyzes misfolding of protein...

Maybe with nanotechnology something could be recovered from what's left after CJD? But my rough impression is that brain tissue is being thermodynamically scrambled. Its probably a matter of degree but at some point you might be "making up" what the brain was like, rather than "measuring" it... and my poorly informed shoot-from-the-hip guess is that CJD leaves behind stuff where you'd be making things up more than measuring them.

About 3 minutes of googling and clicking around trying to find lists of diseases to check into produced Wikipedia's relevant category and a document with one paragraph per disease but no simple list that could be ordered by importance and checked one at a time. Such lists might be fodder for an article if someone were feeling enterprising?