... well that was quite a post, pcflvly. It really laid out in candid and sincere terms the road you've traveled to get to where you are today. I feel like I can almost visualize the whole thing, almost physically, your description was that real.
As so often happens in poly, I don't see any quick or easy answers to the problems here but, I do see little hopeful steps that can be taken one at a time. Listening to (and discussing with him) just a little of her partner's concerns about various things will probably be a "big/little" step in the right direction. Crap I can't remember, have the two of them tried much of any (preferably poly-friendly) counseling together? It seems that the intensity (not to be confused with newness and excitingness) of their feelings for each other has faded like a fire that's burned down to a few faintly-glowing coals. Maybe they don't need "their old NRE" back, but there's something they used to have that seems to need restoration.
You can probably help by at least offering little suggestions here or there when and as long as she solicits them. Unsought advice rarely goes down as well as when a person has directly decided to make themselves vulnerable and hear what you have to say. So you have to wait and watch for those opportunities. And right now, my instinctive thought is, try to especially guide her towards having more closeness (and communication) with her partner again. Paradoxically, her closeness with him is probably the key to the door separating her from you (such as those times when you two long to sleep together but can't very much yet because of his fears/insecurities). So "everybody wins," I guess is what I'm saying, if she can go and/or be guided in this direction.
I now feel that it's somewhat of a mystery as to how much he (her partner) may indeed have a soft spot for polyamory hidden/guarded somewhere safely in the vaults of his heart despite his swinging history with her. Kind of like my own brother-husband. I think he loves the "feel and ideals" that poly represents; yet "living the dream" rather scares him sometimes (and used to scare him a lot).
In any case, I can see that you've got much experience to work from with all kinds of responsible non-monogamy (from swinging to free love to poly and more). This is probably why you find yourself in a bit of "the leader role" with respect to your current situation. Your girlfriend and her partner (through her) almost "look to you for the wisdom to figure all this out." Sure they know a lot about polyamory but they probably see you as a guiding source given that you've shared romance so freely for most of your life. They figure you "know how to do it."
Sounds like you've got a pretty full plate, with many responsibilities to juggle. Take time out for yourself sometimes. Your mind (and body) probably needs the rest more than you realize. You carry many burdens on your shoulders (though I see that it's all probably a, "He ain't heavy; he's my brother," type of labor of love for you).
This romance that has come into your life has been a very unexpected blessing, and a very unexpected load to bear at the same time, something you weren't planning on with all the other services you were already engaged in. So you love the work, but it must make you weary from time to time. If you're anything like me you may even sometimes think, "How will I ever get caught up with it all? I hadn't planned on engaging myself this much." Your cup runneth over, as they say ...
You're in a three-person poly situation now. All three persons have to be treated with the same outpouring of love and valuation (this is true of hetero V sitches like mine and yours just as much as it is of full-fledged poly triangle-triads). Try to reach out as much as possible, to both him and her. They may not even realize this, but they both now need you, as in turn you now need both of them in your life.
Good luck, and I am certainly pulling for you here.
P.S. Glad to hear of your compersive delight today. Sometimes polyamory's rewards are slow in coming, but they sure feel awesome once they get there.