Scenerio. I'm playing AVX Cyclops at 100 points and 40pt Jean Grey from WaTX. Cyclops gets hit. Next turn I merge them to GSX Phoenix giving Jean Grey the free action to put them on click #1. If I split them next turn, which click does Cyclops go to? He began the game on click #3. So even though the duo is now on lick #1 am I correct in thinking that Cyclops comes out on click #3 where he started?

Yes. At this point I am unaware of anything that lets a piece pass higher than a lower point starting line it began the game on. If Cyclops took damage and was on click 4 or lower before merge he would be healed back to 3 when split again.

If you look at the text of both the Split and Merge abilities, you can see that they talk about "number of clicks from its starting line" instead of talking about click numbers. This is just for cases like these, where the characters that are splitting/merging have several starting lines.

Thanks for the confirmation!