okay, so my guess is:
system that killed everyone was tempered by the invaders and was activated by the sentence said by River "this world doesn't need to exist"
its apperance was River because is was created with his mana, so it took over his body(?) on the harvest day
the one we see now is uncorrupted system, that saved scanned consciousness of everyone from Taibern that died that day
as for the system using Elisa's apperance it's because Elisa was not in the system so she is not there, and who we see now is daughter/son of River that he created
As for Jumper, bro is stuck in time loop and just wants out, i guess he saved/destroyed world too many times to care and just wants it to stop