So I was wondering something about split/merge. Lets say I get magneto and professor x on a team and have their duo on the side. magento is at the forefront of my force, taking much of the damage, while professor x has miraculously taken none. I get to a point where i am able to merge the 2 characters. Can I elect to take professor x's click #1 and then split again to have magneto at full health?

Short Answer: Yes
Long Answer: Yesssssss

Depends on which character actually does the Merging. From the PAC:

MERGE
When this character is adjacent to other friendly characters that each represent one distinct qualifying character listed on a Duo character’s character card and all of them have no action tokens, give this character a free action to replace all of them with that Duo character, the same number of clicks from its starting line as this character. The combined point value of the qualifying characters must be equal to or greater than the point value of the Duo character (unless that Duo character previously used the Split ability to be replaced by these same characters). The Duo character can’t use the Split ability this turn. This ability can’t be countered.

So if you give Professor X the free action, the duo will be on its starting line. If you give Magneto the free action, it will be however many clicks deep into its dial that Magento was.

I used to do that all the time with Superman and Wonder Woman... I might have to get that figure out again.

It can be a dirty trick (make sure you follow the instructions that Norm gave above or it won't work the right way), but it's totally legal. I actually enjoyed doing that with my Mr. Miracle/Oberon Duo and keeping my Oberon Bystander back in my starting area while the SLOSH Mr. Miracle went out into the battlefield to cause annoyance. Took my opponent literally more than 7 turns (after focusing on him) just to land a hit on Mr. Miracle that stuck after Oberon "healed" him and they KO'd Oberon.