The only issue with listening to the Companion Chronicles with these timelines is that the primary story sometimes doesn't line up with the order of the secondary post-Doctor arc.

Here's a sort of listening order for the post-Doctor audio stories, with arcs in bold:

• Susan: Here There Be Monsters
• Susan: An Earthly Child, Quinnis, Relative Dimensions, Lucie Miller / To the Death
  • (Eighth Doctor, 8DAs Series 4)

• Ian: The Transit of Venus, The Time Museum (Doctorless), The Revenants

• Vicki: Frostfire

• Sara: Home Truths, The Drowned World, The Guardian of the Solar System
• Oliver: The Perpetual Bond, The Cold Equations, The First Wave
• Steven: The War to End All Wars, The Founding Fathers, The Locked Room

• Polly: The Forbidden Time

• Victoria: The Great Space Elevator, Power Play (Sixth Doctor), The Story of Extinction

• Jamie: The Glorious Revolution
• Jamie: City of Spires, Night's Black Agents, The Wreck of the Titan, Legend of the Cybermen
  • (Sixth Doctor)
• Zoe: Fear of the Daleks
• Zoe: Echoes of Grey, The Memory Cheats, The Uncertainty Principle, Second Chances

• Liz: The Blue Tooth, The Shadow of the Past, The Sentinels of the New Dawn

• Jo: The Doll of Death
• Jo: Find and Replace, The Elixir of Doom

• Sarah: Sarah Jane Smith (spin-off)

• Jago & Litefoot: The Mahogany Murderers
• Jago & Litefoot: Jago & Litefoot (spin-off)
• Jago & Litefoot: The Justice of Jalxar (Fourth Doctor)

• Brewster: The Haunting of Thomas Brewster (not post-Doctor)
• Brewster: The Three Companions (also featuring Polly and the Brigadier)
• ???: The Boy That Time Forgot
• Brewster: Time Reef & A Perfect World (not post-Doctor)

• Nyssa: The Five Companions (also featuring Ian, Steven, Sara, and Polly)
• Nyssa: Circular Time, The Darkening Eye, Cobwebs, etc.
  • Nyssa rejoins the Fifth Doctor in Cobwebs for 15 new adventures

• Tegan: The Gathering

• Peri: Her Final Flight (Sixth Doctor. Also, I know...)
• Peri: Peri and the Piscon Paradox (Fifth Doctor...)
• Frobisher: The Maltese Penguin, The Holy Terror
  • Frobisher rejoins the Sixth Doctor
• Peri: The Widow's Assassin, Masters of Earth, The Rani Elite
  • Peri rejoins the Sixth Doctor

• Benny: Bernice Summerfield (post New Adventures novels)
• Benny/Ace: New Adventures of Bernice Summerfield (Seventh Doctor)

• Ace: The Prisoner's Dilemma (Seventh Doctor, post New Adventures novels)

• Mel: A Life of Crime, Fiesta of the Damned, Maker of Demons
  • Mel rejoins the Seventh Doctor and Ace

• Brigadier: The Spectre of Lanyon Moor (Sixth Doctor)
• Brigadier: Minuet in Hell (Eighth Doctor)
• Brigadier: UNIT (spin-off)
• Brigadier: Old Soldiers
• Yates: The Magician's Oath
• Yates: Hornets' Nest, Demon Quest, Serpent Crest (BBC Fourth Doctor)
• UNIT: Tales from the Vault, Mastermind

• Romana: The Invasion of E-Space
• Romana: The Apocalypse Element (Sixth Doctor)
• Romana: Shada (Eighth Doctor)
• Romana: Neverland, Zagreus (Eighth Doctor, finale to first Charley arc)
• Leela: Jago & Litefoot Series 3-4 (spin-off)
• Romana/Leela: The Worlds of Doctor Who (also featuring, Jago, Litefoot, Yates, & UNIT)
• Romana/Leela: Gallifrey Series 1 (spin-off)
• Romana: The Chaos Pool (Fifth Doctor, finale to Key2Time trilogy)
• Amy & Zara: Graceless (spin-off)
• Romana/Leela: Gallifrey Series 2-6 (spin-off)
• Romana/Ace: Gallifrey Series 7 (spin-off)
• Romana: Luna Romana
• Romana/Leela/Ace: Gallifrey Series 8 (spin-off)
• Leela: Casualties of War (War Doctor)
• Leela: The Catalyst, Empathy Games, The Time Vampire, The Child