It sounds like you should spend more time with your son. It is good for you, it is good for him. I have come so much closer with my daughters over this past year and I am grateful for it. I am a better dad now than I was a year ago, and it is the improvement that I am most proud of.
It sounds like you are doiing well. I think the affection after her being angry is a very good sign. Be a gentleman, but continue to GAL.
I am not sure saying to your W that your S needs to get use to not seeing you is a good idea though. Let her know that you will fight for every minute of his time. Believe me, I was a little apprehensive of taking D5 & D3 by myself for 50% of the time at first (I wasn't sure how well I would handle it); but now I will have it no other way.