Firstly, Uncanny Avengers Vol. 3 #5-6. The stories indicate that:
1. Synapse took a break after the death of her grandfather.
2. Cable was basically hanging constantly with the team.
After those issues Synapse is back with the team and Cable goes to fix his time-travel tech. Currently, Black Knight Vol. 4 and Squadron Supreme Vol. 4 #2-3 which feature Unity Division with Synapse and without Cable sit between UA3 #4 and #5 which doesn't really make sense. Reading through almost everything (I've only skipped everything GotG related, Red Wolf and HtD main story) I haven't really seen anything that would force such late placement. So, UA3 #5-6 should be moved before those.
Speaking of which, that's some heavily unnatural cluster of "going to Weirdworld" stories. I can't really follow direct time references out of that list well, but shouldn't it be possible to uncluster those at least partially?
The second thing I wanted to mention is Standoff. The exact timeline is in the separate thread, but since it is relevant to this I will just comment on it wholesale here and only quote the post here for notifications sake.
StrayLamb wrote: ↑Thu Apr 26, 2018 2:45 amchronology for Avengers Standoff: Assault on Pleasant Hill
The two chronologies are currently inconsistent with each other.
To put the compressed version of the current Standoff chronology into the context of this chronology:
HCSHIELD 1-5 (shortly before Standoff!)
CASW 4-6 (2-3 weeks after CASW 1-3)
NA4 7
TAH 1-4
NO6 5-6
DD5 1-5
HTD5 1-3 (Gwenpool backups)
GP SPEC (Spider-Woman pregnant): Christmas Eve
ILLUM 1-5 (right before Standoff!)
AOSHIELD 1-2 (lead-in to Standoff!)
Avengers Standoff: Welcome to Pleasant Hill 1
Howling Commandos of SHIELD 6 (8-9)
Uncanny Avengers 7 (1-3)
Avengers Standoff: Assault on Pleasant Hill Alpha 1 (1-5)
Agents of SHIELD II 1
Agents of SHIELD II 2
Agents of SHIELD II 3 (1-5:3)
All-New, All-Different Avengers 7 (1-3)
Avengers Standoff: Assault on Pleasant Hill Alpha 1 (6-30)
Howling Commandos of SHIELD 6 (1-7)
Avengers Standoff: Assault on Pleasant Hill Alpha 1 (31-34)
Captain America: Sam Wilson 7/1 (12-21:4)
All-New, All-Different Avengers 7 (4-11)
Captain America: Sam Wilson 7/1 (21:5-28)
Captain America: Sam Wilson 7/1 (1-5)
Uncanny Avengers 7 (4-19:1)
All-New, All-Different Avengers 7 (12-13)
Uncanny Avengers 7 (19:2-20)
All-New, All-Different Avengers 7 (14-20)
Captain America: Sam Wilson 7/1 (29-33)
Captain America: Sam Wilson 7/1 (6-11)
Captain America: Sam Wilson 7/1 (34-40)
Uncanny Avengers 8
All-New, All-Different Avengers 8 (1-18)
Captain America: Sam Wilson 8 (1-19:3)
All-New, All-Different Avengers 8 (19-20)
Captain America: Sam Wilson 8 (19:4-20)
Avengers Standoff: Assault on Pleasant Hill Omega 1(1-24)
Avengers Standoff: Assault on Pleasant Hill Omega 1 (29:6-30)
Agents of SHIELD II 3 (5:4-18)
New Avengers 8 (1-10)
Agents of SHIELD II 3 (19-20)
New Avengers 8 (11-17) ~ Agents of SHIELD 4 (1-9)
Agents of SHIELD II 4 (10-13)
New Avengers 8 (18-19) ~ Agents of SHIELD 4 (14-17)
Agents of SHIELD II 4 (18-20)
Agents of SHIELD II 5
Agents of SHIELD II 6
New Avengers 8 (20)
New Avengers 9
New Avengers 10
Illuminati 6
Avengers Standoff: Assault on Pleasant Hill Omega 1 (25-26, 28-29:4, 31-32:4)
Avengers Standoff: Assault on Pleasant Hill Omega 1 (32:5-34)
Avengers Standoff: Assault on Pleasant Hill Omega 1 (27)
AOSHIELD 5-6 (aftermath of Standoff!)
ILLUM 7 (right after Standoff!)
So the first thing:
Howling Commandos of SHIELD 6 (8-9) happens between HCSHIELD 3 and 4. There is no reason for Duggan to delay getting Orrgo back after he learned that Kraye shipped him off and why (so maybe one, maybe few days max.), so HCSHIELD 1-5 should probably be moved just before the event proper.
The second thing is the placement of the Agents of SHIELD which is doubled and somewhat different between the outer and inner chronology. I would say the placement for the beginning is right in the Standoff chronology, but there is a matter of how the later issues are placed in regards to the New Avengers.
Basically, AOS follow here directly from their confrontation with NA and NA issues are put later. But, AOS #6 which has to follow directly from #5 show heroes who were involved into Pleasant Hills situation outside of it, so the crisis had to be resolved already.
Meanwhile, at around the end of New Avengers #10 we are told by Duggan that Hill's status is still unknown, so it has to happen while the crisis is still ongoing.
This creates a problem with the Avengers Standoff: Assault on Pleasant Hill Omega where it is shown that the SHIELD agents outside didn't know about the crisis until they received the distress signal and then SHIELD appears Duggan included, but since they had to know anyway due to HCSHIELD, I would say let's ignore that detail and just put the NA10 (of course with stuff leading to it) before SHIELD air raid.
And the last thing - everything else has precisely placed flashbacks, but Illuminati 6 doesn't. There is another contradiction here. In AS:AoPHO, Absorbing Man is shown fighting against the Avengers in the combat montage, int Illuminati he runs away instantly when he sees them arriving and meets Hood and Titania who take him and Whirlwind away. I would ignore the montage, as he is a background character here.
So taking into account that Avengers Standoff: Welcome to Pleasant Hill happens over a long time, and Zemo has to prepare the revolt, the beginning after shifting should go:
CASW 4-6 (2-3 weeks after CASW 1-3)
NA4 7
TAH 1-4
NO6 5-6
DD5 1-5
HTD5 1-3 (Gwenpool backups)
GP SPEC (Spider-Woman pregnant): Christmas Eve
Avengers Standoff: Welcome to Pleasant Hill 1
HCSHIELD 1-5 (shortly before Standoff!) + Howling Commandos of SHIELD 6 (8-9)
ILLUM 1-5 (right before Standoff!)
Uncanny Avengers 7 (1-3)
Avengers Standoff: Assault on Pleasant Hill Alpha 1 (1-5)
Agents of SHIELD II 1
Agents of SHIELD II 2
Agents of SHIELD II 3 (1-5:3)
All-New, All-Different Avengers 7 (1-3)
But I'm not sure about the exact splitting of AS:AoPHO to place NA and partially AoS there and about the exact place for Illuminati flashbacks.