I think the brain functioning part is explained by the Z-space thing.
As for everything else....maybe when a morpher morphs, everything happens at a cellular level, maybe even atomic level. Like all of that person's atoms are functioning by themselves as individual atoms and don't function for any particular purpose (like supporting organs, supplying blood), and when the morph is complete, then it comes back to function as a literal being. Communication between atoms would have to be through philotic links. ^^
This could also explain why morphing technology works for every species (at least the ones we know of).