I would advise you let them interact more and sort out the trouble each one is having with the other on their own. It isn't helpful if you stand in between them all the time, as an obstacle or mediator. This leads to an unhealthy dynamic as they need to re-form their former friendship as well.
It seems the progress you are making, is too fast. Everyone should be comfortable with the other (including the two guys) and as long as Y is struggling and E isn't aware of his perspective, things are bound to become more dramatic bit by bit. There are some things you can't 'fix'. And the work that has to be done right now, isn't on your plate. All you can do right now is watch out for both of them, keep the current level and wait for them to come to some kind of understanding. Encourage them to keep more in touch and check in regularly with the other and to not mediate their problems over you exclusively. I have a hard time with withdrawing as well. I don't feel comfortable when not in control. But those problems are theirs to sort out.
When our v began living together last year, there were many talks I just wasn't involved in. They needed those times to set the boundaries of their relationship. It is important that everyone is able to speak up for himself and knows how to communicate with everyone involed in the relationship(s). Don't become their spokesperson, this won't do you or them any good.
Facts: 30, female, bi, v-type relationship with Sward (husband, straight, mono) and Lin (boyfriend, straight, mono), poly-fi and co-primary.