Starting over wasn't that bad. I have a quick question tho : what's the point of the "Rebirth Operation" ? Besides a new portrait/body, scenes seems unaffected by it.
if you have chossen share house and completed kira she should be among the people to talk to to be your roommate and riley should be there by default (to have more than 1 roommate you need the share house) if you have that and finished kira talk to one person ask them to be your roommate and then choose to someone else