It does sound like you are still healing from the past, even though you have reached a good place in your marriage again. I wonder if there is something about this woman that makes you insecure and less confident than you normally would be. You said that when you first began with poly, "I was very insecure about him developing a relationship with this friend, because I knew they had a deep connection." That would seem to indicate that you are comfortable with only a certain amount of emotional investment for your husband to make, but you don't really want him to have a deep connection.
Granted, he went out of control, but if I were you I never would have left the house with the kids for him to boink her while you were out. So you did participate in the craziness by stepping aside instead of shaking him and saying you weren't comfortable with that. So, now here you are in Round 2, and you've begun to make observations that are all too familiar. Whether you are being a bit paranoid about history repeating itself or not, it sounds like you are isolating yourself and trying to figure things out on your own. To me, that would be almost the same mistake you made before by not standing up for yourself when he was wrapped up in his excitement (NRE?).
From all the reading I've done, this would seem to be a case of needing more communication among all of you. Don't let it get away from you this time. If you need it to slow down or limit his time with her, I would think you should have every right to ask for that. You and your husband would also probably benefit from regular ongoing meetings with her and her husband, to work things out so that it is all much more manageable. Figure out what boundaries that all of you can live with. Just my two newbie cents.