Here you go, The List so far.
(I'm still working on placing MTMTE #39-42, but ignore that for now.)
I. The Beginning…1. Megatron Origin
2. Spotlight - Orion Pax
3. Spotlight – Blur (All Hail Megatron Vol. 3 p. 4)
4. Autocracy
5. Monstrosity
6. Primacy in 2014
7. Spotlight - Thundercracker
II. The Spotlights8. Spotlight – Shockwave (Spotlight Vol. 1 p. 9)
9. Spotlight – Cliffjumper (All Hail Megatron Vol. 3 p. 52)
10. Spotlight – Soundwave (Spotlight Vol. 2 p. 9)
11. Spotlight – Wheelie (Spotlight Vol. 3 p. 100)
12. Spotlight - Hot Rod (Spotlight Vol. 1. p. 50)
13. Spotlight – Sixshot (Spotlight Vol. 1 p. 73)
14. Spotlight -- Ultra Magnus (Spotlight Vol. 1 p. 96)
III. Present Day Earth15. Infiltration #0-3 (through p. 86)
16. Stormbringer #1-3
17. Infiltration #4-5 (p. 87-132)
18. Stormbringer #4 (Full page panel of Thunderwing in jet mode)
19. Infiltration #6 (p. 133 to end)
20. Spotlight – Kup (Spotlight Vol. 2 p. 28)
21. Escalation #1-2 (through p. 46)
22. Spotlight – Nightbeat (Spotlight Vol. 1 p. 27)
23. Escalation #3-6 (p. 47 to end)
24. Spotlight – Ramjet (Spotlight Vol. 2 p. 100)
25. Spotlight - Optimus Prime (Spotlight Vol. 2 p. 76)
26. Spotlight – Galvatron (Spotlight Vol. 2 p. 52)
27. Devastation #1-4 (pages unnumbered; Chapter 4 ends with close-up of Starscream talking to Astrotrain)
28. Spotlight – Blaster (Spotlight Vol. 3 p. 4)
29. Spotlight – Arcee (Spotlight Vol. 3 p. 28)
30. Devastation #5-6 (pages unnumbered; Chapter 5 begins with “Cybertron-The Past”)
31. Spotlight – Mirage (Spotlight Vol. 3 p. 76)
32. Spotlight – Grimlock (Spotlight Vol. 3 p. 52)
33. Spotlight Volume 4 – Revelation
34. Maximum Dinobots
IV. All Hail Megatron!35. All Hail Megatron Vol. 2 Chapter 2 p. 1
36. All Hail Megatron Vol. 2 Chapter 1 p. 3-13, 17-19
37. All Hail Megatron Volume 4: “Everything In Its Right Place”
38. Spotlight – Drift (All Hail Megatron Vol. 3 p. 76)
39. Spotlight – Metroplex (All Hail Megatron Vol. 3 p. 100)
40. All Hail Megatron Volume 4: “Lost And Found”
41. Spotlight- Jazz (All Hail Megatron Vol. 3 p. 28)
42. All Hail Megatron Volume 1-2 in full
(Note: All Hail Megatron Volume 4 has #43-#48)
43. “Old Ways” Optimus/Ironhide
44. “Uneasy Lies The Head” Starscream
45. “Replay” Sunstreaker
46. “Rebirth” Galvatron/Cyclonus/Scourge
47. “The Man Of Steel” Spike
48. “Hidden” Bumblebee
V. Three Years Later (Note: #50-#58, #68-#72 are located in Last Stand Of The Wreckers Hardcover)
49. Spotlight- Prowl (Ongoing Vol. 6)
50. Autobot File: Rotorstorm p. 130
51. Autobot File: Pyro p. 131
52. Autobot File: Guzzle p. 132
53. Autobot File: Ironfist p. 133
54. Autobot File: Impactor p. 134
55. Decepticon File: Snare p. 135
56. Decepticon File: Overlord p. 136
57. Squadron X p. 161
58. BULLETS/OUT OF BULLETS: Deleted Scenes p. 116 - 128 except ‘Nine Months Later’
59. Last Stand Of The Wreckers #1
60. Ongoing Vol. 1 For All Mankind #1
61. Last Stand Of The Wreckers 2-3
62. Ongoing Vol. 1 #2
63. Last Stand Of The Wreckers 4
64. Ongoing Vol. 1 #3-4
65. Bumblebee paperback
66. Ongoing Vol. 1 #5-6
67. Last Stand Of The Wreckers 5
68. ESCAPE p. 162
69. ZERO POINT p. 170
70. IN WORD AND DEED p. 175
71. BULLETS: Nine Months Later p. 125
72. Wreckers Mosaic Dead Man’s Boots p. 129
73. Ironhide paperback
74. Drift paperback
75. Ongoing Vol. 2 International Incident (#7-#8)
76. Ongoing Vol. 4 Heart Of Darkness.“The Road To CHAOS”. Infestation occurs towards end of #4. End of #4 lines up with end of Ongoing #20 in Ongoing Vol. 5: Chaos Theory.
77. Infestation Transformers 1-2
80. Ongoing Vol. 2 #9 to #12
81. Ongoing Vol. 3 Revenge of the Decepticons #13
82. Spotlight - Megatron
83. Ongoing Vol. 3 remainder of Revenge Of The Decepticons
84. Ongoing Vol. 5 Chaos Theory through end of Police Action: Prolog
85. Spotlight - Bumblebee
86. Ongoing Vol. 6 Police Action
87. Ongoing Vol. 5 remainder of Chaos Theory
88. Ongoing Vol. 7 CHAOS
89. Death Of Optimus Prime (More Than Meets The Eye Vol. 1)
VI. The Autobots Divide90. More Than Meets The Eye Ongoing #1 with Rodimus (Vol. 1)
91. Robots In Disguise Ongoing #1 with Bumblebee (Vol. 1)
92. MTMTE #2-3 (Vol. 1)
93. RID #2-3 (Vol. 1)
94. MTMTE #4-5 (Vol. 2)
95. RID #4-5 (Vol. 1)
96. Spotlight – Trailcutter(Trailbreaker renamed)
97. Spotlight – Hoist
98. More Than Meets the Eye #6 (Vol. 2)
99. More Than Meets the Eye Annual 2012 (Vol. 3)
100. More Than Meets the Eye #7-8 (Vol. 2)
101. Robots in Disguise #6-10 (Vol. 2, 3)
102. More Than Meets the Eye #9-13 (Vol. 3, 4) and text story “A Signal To Noise” (Vol. 4)
103. Robots in Disguise Annual 2012 (Vol. 3)
104. Robots in Disguise #11-16 (Vol. 3, 4)
105. More Than Meets the Eye #14-15 (Vol. 4)
106. Robots in Disguise #17-20 (Vol.5)
107. More Than Meets the Eye #16-21 (Vol. 4, 5) and text story “The Sound Of Breaking Glass” (Vol. 5)
108. Robots in Disguise #21-22 (Vol. 5)
109. More Than Meets the Eye #22 (Vol. 5)
VII. Dark Cybertron110. Dark Cybertron (Voll. 1-2)
VIII. Dawn of the Autobots111. Robots in Disguise #28-32
112. More Than Meets the Eye #28-34
113. Windblade #1-4
114. Robots in Disguise #33-34
115. Drift: Empire of Stone
IX. Days of Deception116. The Transformers #35-38
117. More Than Meets the Eye #35-38
118. Transformers: Punishment
Xa. Combiner Wars118. The Transformers #39
119. Windblade #1
120. The Transformers #40
121. Windblade #2
122. The Transformers #41
123. Windblade #3
124. The Transformers #42
125. Windblade #4
Xb. ??
126. More Than Meets the Eye #39-42