The main section on what comics were in what section of the story is mainly sourced from the Clone Saga Reading Order found at the bottom of the Marvel Wiki at Fandom.com - here's a link to the one for the first issue: https://marvel.fandom.com/wiki/Web_of_Spider-Man_Vol_1_117#Notes. The same site also has a good page for the entire event: https://marvel.fandom.com/wiki/Clone_Saga_(Event)
The books have been sourced by scouring through previews online catalog, which is an excelent resource for older trades - https://www.previewsworld.com/Search?mode=A&q=clone%20saga&Category=3.
ACT ONE
Power and Responsibility
Web of Spider-Man #117
Amazing Spider-Man #394
Spider-Man #51
Spectacular Spider-Man #217The Exile Returns
Web of Spider-Man #118
Spider-Man Unlimited #7
Spider-Man #52
Web of Spider-Man #119
Spider-Man #53Back From the Edge
Spider-Man Unlimited #7
Amazing Spider-Man #395
Spectacular Spider-Man #218
Amazing Spider-Man #396
Spectacular Spider-Man #219Web of Life
Web of Spider-Man #120
Spider-Man #54
Web of Spider-Man #121
Spider-Man #55Web of Death
Amazing Spider-Man #397
Spectacular Spider-Man #220
Amazing Spider-Man #398
Spectacular Spider-Man #221Funeral for an Octopus
Spider-Man Unlimited #8
Spider-Man:Funeral for an Octopus #1
Spider-Man:Funeral for an Octopus #2
Spider-Man:Funeral for an Octopus #3Smoke and Mirrors
Web of Spider-Man #122
Amazing Spider-Man #399
Spider-Man #56
Spider-Man:The Clone Journal #1Players and Pawns
Spectacular Spider-Man #222
Web of Spider-Man #123
Amazing Spider-Man #400Aftershocks
Spider-Man #57
Spectacular Spider-Man #223The Lost Years
Spider-Man:The Lost Years #1
Spider-Man:The Lost Years #2
Spider-Man:The Lost Years #3
Spider-Man:The Lost Years #0Mark of Kaine
Web of Spider-Man #124
Amazing Spider-Man #401
Spider-Man #58
Spectacular Spider-Man #224
Spider-Man Unlimited #9Crossfire
Web of Spider-Man #125
Amazing Spider-Man #402
Spider-Man #59
Spectacular Spider-Man #225The Trial of Peter Parker
Web of Spider-Man #126
Amazing Spider-Man #403
Spider-Man #60
Spectacular Spider-Man #226Planet of the Symbiotes
Amazing Spider-Man Super Special #1
Spider-Man Super Special #1
Venom Super Special #1
Spectacular Spider-Man Super Special #1
Web of Spider-Man Super Special #1
ACT TWO
Maximum Clonage
Spider-Man:The Jackal Files #1
New Warriors #61
Spider-Man:Maximum Clonage Alpha #1
Web of Spider-Man #127
Amazing Spider-Man #404
Spider-Man #61
Spectacular Spider-Man #227
Spider-Man Maximum Clonage:Omega #1New Warriors
New Warriors #62
New Warriors #63
New Warriors #64
New Warriors #65
New Warriors #66Growing Pains
Amazing Spider-Man Super Special #1
Spider-Man Super Special #1
Venom Super Special #1
Spectacular Spider-Man Super Special #1
Web of Spider-Man Super Special #1The Exiled
Web of Spider-Man #128
Amazing Spider-Man #405
Spider-Man #62
Spider-Man Unlimited #10Time Bomb
Spectacular Spider-Man #228
Web of Spider-Man #129The Greatest Responsibility
Amazing Spider-Man #406
Spider-Man #63
Spectacular Spider-Man #229
Spider-Man:The Parker Years #1
ACT THREE
Virtual Morality
Scarlet Spider Unlimited #1
Web of Scarlet Spider #1
Amazing Scarlet Spider #1
Scarlet Spider #1
Spectacular Scarlet Spider #1Cyberwar
Web of Scarlet Spider #2
Amazing Scarlet Spider #2
Green Goblin #3
Scarlet Spider #2
Spectacular Scarlet Spider #2Nightmare in Scarlet
Web of Scarlet Spider #3
New Warriors #67
Web of Scarlet Spider #4The Sensational Spider-Man
Wizard Mini-Comic #3
Sensational Spider-Man #0
Amazing Spider-Man #407
Spider-Man #64
Spectacular Spider-Man #230
Spider-Man Unlimited #11The Final Adventure
Spider-Man:The Final Adventure #1
Spider-Man:The Final Adventure #2
Spider-Man:The Final Adventure #3
Spider-Man:The Final Adventure #4
ACT FOUR
The Clone Saga has bern collected across four Omnibuses which are due to be reprinted in 2024:Media Blizzard
Sensational Spider-Man #1
Amazing Spider-Man #408
Spider-Man #65The Return of Kaine
Spectacular Spider-Man #231
Sensational Spider-Man #2
Amazing Spider-Man #409
Spider-Man #66
Spectacular Spider-Man #232Web of Carnage
Sensational Spider-Man #3
Amazing Spider-Man #410
Spider-Man #67
Spectacular Spider-Man #233Blood Brothers
Sensational Spider-Man #4
Amazing Spider-Man #411
Spider-Man #68
Spectacular Spider-Man #234
Sensational Spider-Man #5
Amazing Spider-Man #412Redemption
Spider-Man:Redemption #1
Spider-Man:Redemption #2
Spider-Man:Redemption #3
Spider-Man:Redemption #4UNNAMED
Spider-Man #69
Spectacular Spider-Man #235
Sensational Spider-Man #6
Amazing Spider-Man #413
Spider-Man #70
Spectacular Spider-Man #236
Spider-Man Unlimited #12Peter Parker Returns
Sensational Spider-Man #7
Amazing Spider-Man #414
Spider-Man #71
Spectacular Spider-Man #237Loose Ends
Amazing Spider-Man #415
Spider-Man #72
Sensational Spider-Man #8
Spectacular Spider-Man #238
Sensational Spider-Man #9
Amazing Spider-Man #416
Spider-Man #73
Spectacular Spider-Man #239
Sensational Spider-Man #10
Amazing Spider-Man #417
Spider-Man #74Revelations
Spectacular Spider-Man #240
Sensational Spider-Man #11
Amazing Spider-Man #418
Spider-Man #75
Spider-Man:Revelations TPB
Osborne Journals #1Aftermath
Amazing Spider-Man '96 #1
Sensational Spider-Man '96 #1
Spider-Man:Hobgoblin Lives #1
Spider-Man:Hobgoblin Lives #2
Spider-Man:Hobgoblin Lives #3
It takes the Clone Saga/Ben Reilly Complete Epics ELEVEN Epic ish size books, all long out of print, to collect the whole Clone Saga:Clone Saga
Omnibus 1
https://www.previewsworld.com/Catalog/JUN231084
ISBN 13: 978-13029-5295-2
ISBN 10: 13029-5295-1Web Of Spider-Man (1985) #117-125
Amazing Spider-Man (1963) #394-401
Spider-Man (1990) #51-58
Spectacular Spider-Man (1976) #217-224
Spider-Man Unlimited (1993) #7-9
Spider-Man: Funeral For An Octopus #1-3
Spider-Man: The Clone Journal And Material From Spider-Man Collectors' Preview.Omnibus 2
NEW PRINTING PREVIEWS LINK
ISBN 13: 978-13029-5584-7
ISBN 10: 13029-5584-5Amazing Spider-Man (1963) #402-406 And Super Special
Spider-Man (1990) #59-63 And Super Special
Spectacular Spider-Man (1976) #225-229 And Super Special
Web Of Spider-Man (1985) #126-129 And Super Special
Venom Super Special
New Warriors (1990) #61-66
Spider-Man: The Jackal Files
Spider-Man: Maximum Clonage Alpha And Omega
Spider-Man Unlimited (1993) #10
Spider-Man Team-Up #1
Spider-Man: The Lost Years #1-3
And Spider-Man: The Parker Years.Ben Reilly
Omnibus 1
https://www.previewsworld.com/Catalog/JUN231086
ISBN 13: 978-13029-5288-4
ISBN 10: 13029-5288-9Web Of Scarlet Spider #1-4
Amazing Scarlet Spider #1-2
Scarlet Spider (1995) #1-2
Spectacular Scarlet Spider #1-2
Scarlet Spider Unlimited #1
Green Goblin #3
Sensational Spider-Man (1996) #0-3 And Wizard Mini-Comic
Amazing Spider-Man (1963) #407-410 And Annual '96
Spider-Man (1990) #64-67
New Warriors (1990) #67
Spectacular Spider-Man (1976) #230-233
Spider-Man/Punisher: Family Plot #1-2
Spider-Man Holiday Special 1995
Spider-Man: The Final Adventure #1-4
Spider-Man Unlimited (1993) #11
Spider-Man Team-Up #2-3 And Material From Venom: Along Came A Spider #1-4.Omnibus 2
NEW PRINTING PREVIEWS LINK
ISBN 13: 978-13029-5582-3
ISBN 10: 13029-5582-9Sensational Spider-Man (1996) #4-11
Amazing Spider-Man (1963) #411-418
Spider-Man (1990) #68-75
Spectacular Spider-Man (1976) #234-241
Spider-Man Unlimited (1993) #12-14
Spider-Man: Redemption #1-4
Daredevil (1964) #354
Spider-Man Team-Up #4-5
Spider-Man: Revelations Tpb (1997) And Spider-Man: The Osborn Journal
101 Ways To End The Clone Saga And Dead Man's Hand.
Amazing Spider-Man Epic 27 The Clone Saga (effectively Clone Saga Epic 1) collectsSpider-Man: The Clone Saga
1 - 424 pagesThe Amazing Spider-Man #3942 - 480 pages
The Spectacular Spider-Man #217
Spider-Man #51–53
Spider-Man Unlimited #7
Web of Spider-Man #117–119
Spider-Man: The Lost Years #1–3The Amazing Spider-Man #395–3993 - 464 pages
The Spectacular Spider-Man #218–221
Spider-Man #54–56
Spider-Man Unlimited #8
Web of Spider-Man #120–122
Spider-Man: Funeral for an Octopus #1–3The Amazing Spider-Man #400–4014 - 480 pages
The Amazing Spider-Man Super Special
The Spectacular Spider-Man #222–224
The Spectacular Spider-Man Super Special
Spider-Man #57–58
Spider-Man Super Special
Spider-Man Unlimited #9
Web of Spider-Man #123–124
Web of Spider-Man Super Special
Spider-Man: The Clone Journal
Venom Super SpecialThe Amazing Spider-Man #402–4045 - 472 pages
The Spectacular Spider-Man #225–227
Spider-Man #59–61
Web of Spider-Man #125–127
New Warriors #61
Spider-Man: The Jackal Files
Spider-Man: Maximum Clonage Alpha and OmegaNew Warriors #62–64
The Amazing Spider-Man #405–406
The Spectacular Spider-Man #228–229
Spider-Man #62–63
Spider-Man Team-Up #1
Spider-Man Unlimited #10
Venom Super Special Flipbook
Web of Spider-Man #128–129Spider-Man: Ben Reilly
1 - 424 pagesSpider-Man: The Parker Years2 - 424 pages
New Warriors #65–66
Scarlet Spider Unlimited #1
Web of Scarlet Spider #1–2
The Amazing Scarlet Spider #1–2
Scarlet Spider #1–2
The Spectacular Scarlet Spider #1–2
Green Goblin #3
The Sensational Spider-Man #0
Sensational Spider-Man Mini-ComicAmazing Spider-Man #407–4083 - 432 pages
New Warriors #67
Sensational Spider-Man #1
Spectacular Spider-Man #230
Spider-Man #64–65
Spider-Man/Punisher: Family Plot #1–2
Web of Scarlet Spider #3–4
and material from: Spider-Man Holiday Special
Venom: Along Came a Spider 1–4Amazing Spider-Man #409–4104 - 464 pages
Sensational Spider-Man #2–3
Spectacular Spider-Man #231–233
Spider-Man #66–67
Spider-Man: The Final Adventure #1–4
Spider-Man Team-Up #2
Spider-Man Unlimited #11Amazing Spider-Man #411–4135 - 464 pages
Sensational Spider-Man #4–6
Spectacular Spider-Man #234
Spider-Man #68–70
Spider-Man Team Up #3
Spider-Man Unlimited #12
Spider-Man: Redemption #1–4Amazing Spider-Man #414–416 and material from: Annual '966 - 448 pages
Sensational Spider-Man #7–10
Spectacular Spider-Man #235–239
Spider-Man #71–72
Spider-Man Team Up #4
Spider-Man Unlimited #13Amazing Spider-Man #417–418
Sensational Spider-Man #11
Spectacular Spider-Man #240- 241
Spider-Man #73–75
Spider-Man Team-Up #5
Spider-Man Unlimited #14
Spider-Man: Revelations extra pages
Spider-Man: The Osborn Journal #1
101 Ways to End the Clone Saga #1
Spider-Man: Dead Man's Hand #1
Web of Spider-Man (1985) 117-119That's all of Clone Saga The Complete Epic book 1 and a portion of 2.
Amazing Spider-Man (1963) 394-396
Spider-Man (1990) 51-53
Spectacular Spider-Man (1976) 217-219
Spider-Man Unlimited (1993) 7
clone subplot pages
Amazing Spider-Man Epic 28 Web of Life, Web of Death collects
Amazing Spider-Man #397-399That's the rest of Clone Saga The Complete Epic book 2 and a small portion of 3.
Spectacular Spider-Man #220-222
Web of Spider-Man #120-123
Spider-Man #54-56
Spider-Man Unlimited #8
Spider-Man: Funeral for an Octopus #1-3
Spider-Man: The Clone Journal
I can't see Epics collecting the complete saga in less than NINE books.
