I was curious so I just checked that route.
1) Jack says "She was good company during my runs." and "I think her paranoia rubbed off on me – like a drug.", haven’t seen anything about his grades.
2) The next day, if you try to enter the school bathroom, it will say "That fucking cunt must be in there with her…" which implies NTR to me.
Neither it’s irrefutable evidence, but it’s good enough for me.
By the way, if anyone is wondering how the progress on the next update is coming along… the last time Geeseki checked off one of his tasks was June 4. (The writer and the coder did some small stuff, but that’s all.)