If the separation is working, then it is a good thing. Such a simple and powerful phrase: Do what works!
And I can see that it would be difficult to live in each other's pockets and still be working through not only personal issues but issues that you experienced as a couple, especially as you were long distance for so long.
Those of us in long term, long distance relationships are quite independent and I confess even now, I wonder how I would go back to living with someone full time. Sometimes there is no better feeling after a long hard day than to go home and know that only my cat is there with no more demand than to put food in her dish.
I am glad to hear you are both having fun as well as still attending counselling. Have a great weekend and pop back with updates when you can!