Thanks for the tips. I've updated the list according to that information and it seems to make more sense now. It's missing a few Trainer reprints (Reversal, Poke Ball, etc.) from the Battle Starter Decks; however, everything seemed to fall into place:
HOLO
1. Jirachi
2. Magmortar
3. Manaphy
4. Metagross
5. Ninetales
6. Octillery
7. Politoed
8. Shaymin
9. Sudowoodo
10. Xatu
RARE
11. Beedrill
12. Blastoise
13. Cherrim
14. Crobat
15. Fearow
16. Floatzel
17. Kingdra
18. Leafeon
19. Mismagius
20. Poliwrath
21. Primeape
22. Raichu
23. Roserade
24. Steelix
25. Torterra
26. Tyranitar
27. Ursaring
UNCOMMON
28. Carnivine
29. Golbat
30. Grotle
31. Kakuna
32. Lanturn
33. Lucario
34. Metang
35. Minun
36. Onix
37. Plusle
38. Poliwhirl
39. Pupitar
40. Pupitar
41. Seadra
42. Wartortle
COMMON
43. Aipom
44. Beldum
45. Buizel
46. Cherubi
47. Chinchou
48. Dunsparce
49. Eevee
50. Horsea
51. Larvitar
52. Larvitar
53. Mankey
54. Misdreavus
55. Natu
56. Numel
57. Pikachu
58. Poliwag
59. Remoraid
60. Riolu
61. Roselia
62. Spearow
63. Squirtle
64. Stantler
65. Teddiursa
66. Torkoal
67. Tropius
68. Turtwig
69. Vulpix
70. Weedle
71. Zubat
T/S/S
72. Cheerleader’s Chant
73. Defender
74. Dual Ball
75. Engineer’s Adjustments
76. Good Rod
77. Interviewer’s Question
78. Judge
79. MC’s Chatter
80. PlusPower
81. Pokemon Circulator
82. Rare Candy
83. Super Scoop Up
PRIME
84. Crobat Prime
85. Kingdra Prime
86. Lanturn Prime
87. Steelix Prime
88. Tyranitar Prime
89. Ursaring Prime
LEGEND
90. Entei/Raikou LEGEND
91. Entei/Raikou LEGEND
92. Entei/Suicune LEGEND
93. Entei/Suicune LEGEND
94. Raikou/Suicune LEGEND
95. Raikou/Suicune LEGEND
SR
TWO. Alph Lithograph (Shuffle Your Deck)
All of these are either left over from HG/SS, in the Battle Starter Decks/Expert Deck Leafeon vs. Metagross, or make up the T-Tar/Steelix/LEGEND line.