1: Why do the Separatists want Amidala dead if she is the one opposing a military response to the Separatists, and as such is the closest thing to an ally that they have?
It’s made pretty clear that it’s just Nute Gunray seeking petty revenge for the events of the last film.
4: Why does the Republic not know about the army that they ostensibly ordered? Did the cloners not bother to get any confirmation or send any updates?
While it is somewhat unlikely, the idea of it getting lost in bureaucracy over a decade is humorously plausible.