a) The Vishnans are energy being... It's hinted in BP that the Shivans are something similar...Possibly Energy being who can take solid form...Like Lorien or the Vorlons in B5
This could actually be a good explenation for the mechanoid aspects of the shivans. Those bodies are actually encounter suits that are "inhabited" by the Shivans either beause their energy bodies can't interact otherwise with physical beings, or to hide their true nature.
c) Samuel Bei was turned into a "sorta-vishnan" - energy being but not quite part of the Vishnan conciensness...but it gained the Vishnan's a better understanding of humanity. Possibly he could have bridge between the Vs and humanity...A sort of Locutus-of-Borg.
Samuel wasn't changed. They took his spirit/mind/personality/whatever and projected or even moved it into a ship. But his body remained as it was, stored (kinda) safely in the Keeper. That he returned to his body after the Keeper was destroyed, makes it more likely that he was only projected and not completely moved into the ship.
4) Shivans and Vishnans are not Seperate species...They are different Aspects of the SAME race...
I'll explain this in a seperate thread soon...It's Vorlon related, so it will be complecated...
Not too complicated. One faction wanted to best the Shadows within the rules, while the other thought pretty much "screw those stupid rules and just wipe out anyone touched by the shadows".