1. I assumed the Borg's memories of their own origins were damaged. In any event, this might be an "inconsistency" but is hardly a "plot hole", and if that's enough to damage your opinion of the trilogy then I don't think the problem lies with the books.
Yep, Borg didn't remember their own origins, and what with those origins being a mad, dying Caeliar and panicked, starving humans, and millenia ago, is understandable. (This from the authors, after I posted about my plot hole about a year ago - why did the Borg try to undo First Contact, if it would undo their own inception?)
The Caeliar probably learned time travel after being hurled back through time. Harnessed, this ability allowed them to build their spheres in no time at all.