Assuming I'm interpreting things correctly: if Thothandal is a fused AI, and the Jjaro in this theory are innumerable instances of this same fused AI, how do (what I remember of your interpretations of) Yrro and Pthia fit into things? Since I don't think two fused AIs would need to balance each other out, what with balancing themselves already.
On a related note: not yet sure how to explain the presence of Thothandal's insignia on the Jjaro ships, but I figure that his regular appearances in the dream levels are due in part to space-time weirdness, and in part because he's the only person who can help the SO seal the W'rkncacnter and end this madness.
(The latter is how I speculate that Durandal figured out how to activate Thoth a lot sooner than he did in M2--he was drawn towards Thoth on a subconscious level. Maybe that would explain why the terminals on "Ne Cede Malis" were displaying Thothandal's texture--Durandal trying desperately to hint at what to do, even if he didn't understand how, exactly?)