what is the main clause in conditional sentences
Solution 1:
Sam will become a husband and a stepfather if he will marry Jane.
The title of your question is 'What is the main clause ...' The answer is that it's the whole sentence. The conditional element, irrespective of interpretation, is an adjunct embedded within the main (matrix) clause .
That aside, the more salient interpretation is that Sam will become both a husband and a stepfather if he marries Jane. The potential for ambiguity is so minimal that it can be discounted.