Only time can tell on many things in life.
The journal is probably a really great idea.
I think some of the issues you have listed make perfect sense. Have you all chosen a poly-friendly therapist? I ask because it might be very helpful if you two could discuss ALL of this (as well as the rest) with the therapist. Even if you resolve whatever the other issues are, if these can't be resolved as well it won't matter...
Just seems like it might be good to address both...
"Love As Thou Wilt"