Answer #1: 8-9-10.
Why?
Yamame. Ya = 8
Iku. Ku = 9
Sanae and Komachi. 3 x 4 = 12. Minus Nitori. 12 - 2 = 10.
Yeah w/e
======================================
Answer #2: Flying.
Why? I I N S K Y.
I IN SKY.
======================================
Answer #3: Elemental or natural affinities.
Iku + Ichirin = Thunderclouds
Nitori + Sanae = Water and Wind, which oppose each other.
Komachi + Yamame = One lives on the "surface", the other lives underground.
======================================
Answer #4: SIKI K-Y
Make of that what you will.
======================================
Miscellanea:
Working with which games they came from, that's 10.5, 12, 10, 10, 9, and 11 respectively.
As for which stages, that's 5, 3, 3, 5, 8, and 1 respectively. (based on Reimu's experiences, anyway)