I think it'll be pretty straight forward:
Quiet Life, Part 1: end with Kira getting stuck inside the box
Quiet Life, Part 2/People of Morioh: end with the Morioh meeting
Sheer Heart Attack: two or three episodes
Atom Heart Father, Part 1: I'm not sure where exactly they'd cut it, to be honest
Atom Heart Father, Part 2: Kira's dad looks around for him, the bird poops onto the Kosaku mailbox, and the second half of the episode is Kira's New Life
then continue on normally with RPS Kid.
I think that's just a bit too slow for the series to end in 39 episodes. How about instead:
21: Kira wants a Quiet Life (ends on Shigechi dying)
22: Kira wants a Quiet Life 2 (people of Morioh + Sheer Heart Attack up to Jotaro being taken out)
23: Sheer Heart Attack 1 (Koichi vs SHA up until Kira personally appears)
24: Sheer Heart Attack 2 (the rest of SHA, ending on Kira escaping)
25: Atomic Heart Father
26: Kira's New Life/The Cat Who Loved Kira 1 (no reason they can't move that arc up)
27: The Cat Who Loved Kira 2 (new opening time!)
28: RPS kid
29: I'm an Alien
30: Highway Star 1
31: Highway Star 2 (I can't see how this fits in a single episode)
32: Transmission Tower
33: Enigma
34: Cheap Trick
35: That's Not My Dad/Bites the Dust 1 (ends on Rohan dying)
36: Bites the Dust 2 (up till Hayato attacks with Stray Cat or when it fails to kill Kira. Maaaaybe when Josuke appears but that's stretching it)
37: Bites the Dust 3/Diamond is Unbreakable 1 (up till Josuke retreats into the house. Aka there is a very natural break point here)
38: Diamond is Unbreakable 2 (up through Okuyasu saving the day)
39: Diamond is Unbreakable 3/END