Just keep it the way it is.
There is no "rule" that a boy HAS TO have his Dad's last name just because he is a boy.
Frankly, you and your Ex are not together anymore... and would'nt you want your son to carry on your name/family name, TOO?
In some cultures, if there are no boys to carry on the family's name... the Husband of the female in the family, will take the last name of his wife.
That is what my Grandpa did. So my last name/my maiden name, is actually the last name of my Grandma. And our family is actually very proud of that... both the men and the women in the family.
Nothing wrong with that.
I would, if I were you, leave your son's last name as is: yours. Less complicated that way, for you. AND you will be getting FULL custody, soon.
My friend, has 3 kids... and they ALL have HER last name. She has boys and girls. Her Ex, is NO longer in the picture, and a current total JERK, and she has since re-married.
Also, I would NOT hyphenate your son's name. Looking down the road... it will be more of a hassle than not. AND, what if one day your Ex is not a very nice Ex anymore... or he is not in your son's life as much... or he remarries or just is not a part of your life/your son's life anymore?
YOU are the custodial parent. Leave your son with your last name.
all the best,
Susan