Here's some data I got for OR Sky Pillar Flags:
674, 792, 1178 CHECKED
750 UNCHECKED (Wallace Unlocking Sky Pillar)
457 UNCHECKED (Defeating Wallace at Sky Pillar)
2735, 2799, 2888 CHECKED (Entering Sky Pillar)
1388 CHECKED (Picking up Sky Pillar Dragon Scale)
725 CHECKED (After listening to all of Rayquaza's Story)
1395 CHECKED (Picking up TM64 [Explosion])
2926 CHECKED
844 UNCHECKED (Before Battling Rayquaza)
217, 604, 704, 713, 722, 724, 753, 844, 883, 928, 930, 953, 2633, 2842, 2925 CHECKED
416, 540, 686, 759, 760, 892, 914, 915, 916, 918, 921, 927, 929, 2926 UNCHECKED (After Capturing Rayquaza and Deoxys, defeating Zinnia, and ending the episode)