I don't want to enter into spoiler territory. But there are two points (besides the initial gain on level 2 if you start the romance)
1) At the date in the restaurant, where you get attacked.
2) After the dinner at Malcolm's house.
If you take the correct choices there, you must have over 80 on romance with Dalton. Now you can proceed with the rest of the story, including the SCS initiation. The relationship seem broken because he rejects you, but surely you noticed, especially at the dinner on Malcolm's house, that you STILL gained romance points there. Something will change on the final mission against Malcolm if you have that score. I need to know at what point you are to tell you.
One clue to the good ending: After the SCS initiation, if you don't see the warped self in the dark world sequence, you're good. Just grind until the 100 job progress points and you'll reach the end of the storyline.