Suppose I have a Wolverine from AvX at 75 points at full health and Cosmic X-23 at full health and I decide to merge both into the duo, what click number would I then be at with the duo?

Depends on the starting line of Cosmic X-23 and who is given the free action to merge.

If they're both on their first click, then they the duo would come in on their first click.

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 char acter (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.

Check the bolded. Whichever character initiated the merge is the one with whom you check clicks from the starting line. Also, note that it it clicks from the starting line not click number.

If the character that's given an action to use merge is on it's starting click the duo will start on it's starting line. Note that merge does not use the actual click number. It is looking at how many clicks the character's dial has moved away from it's starting line.