Here's the Situation (and I hope it makes sense) with 4 questions:

Iron Man MK 7 (IM3 #001) at 75pts is on 4th click (full health?) and War Machine (IIM #029a) at 125pts on it's 5th click, and if i were to merge to 'Iron Man and Warmachine' (IM3 #018 Dual fig)...

would the dual be on the top click or the 4th click due to Iron man being at 75pts (meaning 4th click)?

Is that the same when i split?

and how would that work if i were to split/merge with 'Iron Man and Iron Patriot' Duo (IM3 #017) at 200 pts (6th click)?

Would splitting put both figs on 6th click?

I would also like to know the outcome of each fig in each of the situation if possible.

1. It depends on who is given the action to merge. If MK 7 is given the action the figure will be on its starting line click if WM is given the action the duo will be on the fifth click from its starting line. The number of clicks is counted as the number of clicks from the starting line.

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.

Everything is listed in clicks from the starting line, not click number. Forget about the click number on the figure, just count clicks from the starting line.

#2. IF you had IM/IP on its 200 point starting click and split both figures would be on their respective starting clicks.

and for good measure:

SPLIT
Give this character a power action if it has no action tokens. Replace this character
with one or more qualifying characters each from a different entry listed on
this character’s character card. The qualifying replacement character(s) must
have either qualifying name and total no more than this character’s point value
(unless those characters previously used the Merge ability to be replaced by this
character). Replacement character(s) are assigned an action token and can’t be
given an action this turn. Replacement character(s) begin a number of clicks from
their starting line equal to the number of clicks from this character’s starting line. This ability can’t be countered.

Thank you soo much, that really clears things up!

This is why split and merge reference "starting line" as opposed to click number. When Starting the game at a lower starting line, since you can not pass that line it is essentially the same as being numbered 1, with the exception of the vampire characters that can steal energy above there starting line but that is not a point value situation.

I take it 029a War Machine would not be able to use his trait if he came into the game as a result of a duo split. Am I correct?

VARIABLE THREAT ADAPTATION: At the beginning of the game, choose a standard power. When an opposing character attacking War Machine can use the chosen power, modify its attack and damage values by -1 for that attack.

You are correct.