You say that when they are having probs, you back off "for a day or two." Does that mean that, when everything is hunky-dory, the norm is to be in contact every day?
Perhaps you might consider scaling back your involvement all the time, not just when they are having it rough. Maybe if she knew there was more "space" in his relationship with you, it would help keep things running more smoothly between them.
Do you know whether or not his wife has veto power? If you don't know, find out. Is that possibility what unnerves you?
You expressed near the end of your post a few things that I see as perfectly reasonable to say to your secondary. Specifically, I would tell him this:
"Whenever you two are having issues that need working on, I back off so you can get through it without distraction. I have no problem doing this because I respect your relationship, but - when this is going on, I am never sure what the outcome will be or what is appropriate for me to ask. I don't want to seem selfish but I admit that sometimes I can't help but wonder if my relationship with you is in jeopardy when you two are having trouble. I am glad we worked through things in the past, but I want you to know that there is a part of me that is holding back my feelings for you because I'm afraid it will suddenly end over issues you have with your wife, and I don't want to be completely crushed. I just want you to know how I am affected by what you two go through, and I'm hoping for some reassurance from you about my place in your life."
And see what his response is.