heres another hole in your theory that it was negi going back in time
if he went back in time and gave himself the staff, and only used that staff then even if he were to jump into the past when hes older it still wouldnt explain how he originally got the staff, think about it (sarcastic comment - "magic staffs dont magically appear out of no where!")
another thing is that why would is his companions, if you notice thier actions itd be kinda of obvious
also about how nagi knew his home village was under attack, by what i see, nagi is kinda of a rogue demon hunter (sort of like berserk manga) he probably got some info that the village was going to be attack, i bet he didnt even notice it was his village until he got there
and whats if everyone saying this story is pure harry potter rip off, happy potter sucked, not to mention that time travel storys like these been around long before harry potter...