Just checked the whole list against my own database. These are the cards I am missing, already in your format ^_^
Expedition:
Potion 156/165 {KSS} Errata issued. No reference needed.
Switch 157/165 {KSS}
Majestic Dawn:
Poké Ball 85/100 {KSS}
Noble Victories:
Pawniard 81/101 {KSS} ---> REMOVE
XY:
Venusaur EX 1/146 {XYP}
Blastoise EX 29/146 {XYP}
Shellder 31/146 {GEN}
Cloyster 32/146 {GEN}
Pikachu 42/146 {GEN}
Raichu 43/146 {GEN}
Diglett 58/146 {GEN}
Dugtrio 59/146 {GEN}
Tauros 100/146 {GEN}
Venusaur EX 141/146 {XYP}
Blastoise EX 142/146 {XYP}
XY: Flashfire
Caterpie 1/106 {GEN}
Metapod 2/106 {GEN}
Butterfree 3/106 {GEN}
Charizard EX 12/106 {XYP}
Ponyta 14/106 {GEN}
Rapidash 15/106 {GEN}
Spheal 24/106 {PRC}
Meowstic 43/106 {GEN}
Geodude 45/106 {GEN}
Graveler 46/106 {GEN}
Golem 47/106 {GEN}
Flabébé 63/106 {GEN}
Floette 65/106 {GEN}
Snorlax 80/106 {GEN}
XY: Furious Fists
Magmar 10/111 {GEN}
Jynx 37/111 {GEN}
Machop 44/111 {GEN}
Machoke 45/111 {GEN}
Machamp 46/111 {GEN}
Hitmonlee 47/111 {GEN}
Hitmonchan 48/111 {GEN}
Clefairy 69/111 {GEN}
Clefable 71/111 {GEN}
XY: Phantom Forces
Krabby 13/119 {GEN}
Zubat 31/119 {GEN}
Golbat 32/119 {GEN}
Wobbuffet 36/119 {GEN}
Swirlix 68/119 {GEN}
Diancie 71/119 {GEN}
Fletchling 89/119 {XY Trainer Kit: Latios & Latias}
TPCi Blackstar Promos
N BW100 {FCO}
Xerneas XY05 {STS}
Yveltal XY06 {STS}
Machamp XY13 {GEN}
Champions Festival XY27 {XYP}
Venusaur EX XY28 {XYP}
Blastoise EX XY30 {XYP}
McDonalds Sets [NB: Only legal now is 2015 collection. 2014 collection is marked as legal, this is not correct]
Pikachu 5/12 {GEN}
XY Trainer Kit: Wigglytuff & Bisharp
Clefairy {GEN}
Clefable {GEN}
Potion {BKP}
Tierno {BKP}