Is it the disconnect from our deep subconscious that causes problems communicating with the higher self or are these really two separate pathways?

The way you diagram the linkages between the conscious and the subconscious and higher self is only partly accurate. It is more accurate to represent them as concentric circles, and this is that the channel to higher self separates from the subconscious realm as a separate gateway. So there are two paths once you enter the subconscious, one is internal and the other is external. And both have their mechanisms and their organization and their individual expression within each person as to accessibility and whether the pathways are exercised and are fully open and in use frequently. So in the case of the modern human, the pathways have been suppressed. Both are reduced and the person is left with a limited ability to see beyond the boundaries and consequently, the information that can be returned to them has limits as well. The consequence is the higher self can do less than would otherwise be possible in assisting them, because that linkage is suppressed, although not closed totally. In a similar way, the subconscious is left on its own but rather than sitting on its hands, so to speak, it spends its time largely worrying about what may happen because it is able to connect to the akashic records, and its charter is to defend and protect, so it has a great deal of worry and fear about what may happen to the self but is unable to signal in a robust and detailed way its concerns. So it can give rise to emotional signals and the negative vibrations it creates will result in discord within the body as a further manifestation of this anguish. And so all have consequences. The emotions trigger the stress response and the direct effects on cells can cause all manner of difficulties. So this is one way the subconscious contributes to the karmic manifestation of illness. It transduces its awareness of past failures and threats in seeing a resonance with the current life, as a dark energy of consciousness that can impinge on cellular functioning. And depending on the weak links, and in some cases a target organ related in some way to the back story, the negativity will impinge and cause disarray and give rise to physical symptoms. So this is another compelling reason to reach those deep, deep, levels because this is the instigator of much mayhem within the body, resulting in ill health.