I haven't opened the capx, and I skimmed your post. It sounds like the question is how objects are paired when when no picking is done.
Take this event as an example that does that pairing when there are multiple instances of sprite1 and sprite2.
Every tick
--- sprite1: set position to Sprite2
That is equivelent to the more verbose event here:
Repeat sprite1.count times
Pick sprite1 instance loopindex
Pick sprite2 instance loopindex%sprite2.count
--- sprite1: set position to sprite2
You can replace count with pickedCount instead and that will show what's happening when only some of the objects are picked. Anyways I hope this helps, I thought it was cool when I realized it. If I completely misunderstood then I'll be sure to look at the capx and Re-read your post when I get a chance.
Cheers