I've added numerous issues to the chronology. Some were missing, and others are recently published continuity inserts. Some new volumes were created. See respective volumes for correct placement
in Part 01, Vol. 00 - First Class Origins here
Uncanny Origins #1 (Cyclops)
X-Men Origins: Iceman
X-Men Origins: Jean Grey
in Part 01, Vol. 01 - Children of the Atom here
X-Men Gold (2nd story)
in Part 01, Vol. 02 - Lonely are the Hunted here
X-Men Unlimited #42 (3rd story)
in Part 01, Vol. 05 - The Hidden Years here
Fantastic Four: World's Greatest Comics Magazine #3
in Part 02, Vol. 00 - Second Genesis Origins here (new volume)
X-Men Gold (3rd story)
X-Men Origins: Colossus
in Part 02, Vol. 02 - Rise of the Phoenix here
Girl Comics v2 #1 (6th story)
in Part 02, Vol. 07 - Days of Future Past: Doomsday here (new volume)
in Part 02, Vol. 10 - Live Free or Die here
Marvel Team-Up #117, 118 & 124
in Part 02, Vol. 12 - From the Ashes here
Wolverine by Chris Claremont
Wolverine: Black, White & Blood #4 (1st story)
in Part 02, Vol. 13 - Storm: Blowback here (new volume)
Storm v4 #1-5
in Part 03, Vol. 02 - Kitty Pryde & Wolverine here (new volume)
Wolverine: Exit Wounds (2nd story)
Wolverine and Kitty Pride #1-5
in Part 03, Vol. 03 - The Gift here
Power Pack: Grow Up! (1st story)
in Part 03, Vol. 04 - Worlds of Adventure here
Marvel Fanfare #33
in Part 03, Vol. 08 - Old Soldiers here
Mephisto Vs #1-4
in Part 04, Vol. 08 - Siege Perilous here
Wolverine: Deep Cut #1-4
in Part 04, Vol. 11 - Thick as Thieves here (new volume)
Gambit v6 #1-5
in Part 04, Vol. 12 - Madripoor Knights here (new volume)
Wolverine: Madripoor Knights #1-5
in Part 04, Vol. 13 - Rogue: The Savage Land here (new volume)
Rogue: The Savage Land #1-5
in Part 05, Vol. 20 - A Skinning of Souls here
in Part 06, Vol. 08 - Back to Reality here
in Part 06, Vol. 15 - In the Red Zone here
in Part 07, Vol. 05 - Ghosts from the Past (Part 02) here
X-Force / Cable Annual (1996) (2nd story)
in Part 07, Vol. 06 - Death & Deceit here
Incredible Hulk v2 #455-457
in Part 07, Vol. 15 - Warped Realities here
X-Man #53-55
in Part 11, Vol. 08 - Civil War here
Fantastic Four #539-540
in Part 11, Vol. 09 - The Death of Captain America here
Fallen Son: The Death of Captain America #1-5
in Part 11, Vol. 12 - Thor Returns here (new volume)
Thor v3 #1-3
in Part 13, Vol. 05 - Secret Invasion here
in Part 14, Vol. 15 - Siege here
New Avengers #61, 62 & 64
Thor #610
in Part 15, Vol. 13 - Battle Scars here (new volume)
in Part 21, Vol. 03 - ResurrXion here
I’ll be deleting the previous posts that covered minor additions and crossovers to clean things up and keep the chronology posts as the only focus here.
This post will likely remain up until I add a new one that actually advances the chronology.