Dear Mike,
I know it's difficult but it's important to separate your feelings about the breakup with your wife and the reasons behind it from the issue of preserving a relationship between her and your son. It's important for children to have an ongoing relationship with both parents, and thinking of your wife leaving in terms of 'abandoning' your son doesn't really help you to support this.
Although it is nice to have some one-to-one time with your children, it is probably better to make this the exception rather than the rule. Seeing your parent along with your siblings is more like family life, and having them all together allows it to feel like that to them when they are with you. In any case, if your son doesn't go to his mother's when you have the girls, any one-to-one time with them will be at the expense of excluding him. I know you see him every day, but he will still feel left out if you concentrate on the others when they are with you.
It's not clear to me why you are seeing your daughters for such short periods. Whole alternate weekends are not uncommon for parents of children of this age, so why not go for this? Then you would get proper time with them.
The girls probably don't like you asking them about their mum's boyfriend. I know it is only human, but try and stop as it will upset them and make things harder for you.
Of course you can't force a fourteen year old to see his mother, but you should encourage it if you can. She probably won't see it that way, but you will have more chance of doing this if you give up trying to make him go overnight. Teenagers like to sleep in their own beds (or on the floor at friends' houses) and in my experience have stopped sleeping over at absent parents' houses by this stage even if they did when they were younger. Trying to establish it now is probably not worth the effort, but an evening together every week or so would be reasonable.
Good luck!
Sadie