Thought I’d leave an update with what I’ve done, and the progress.
Replanted the tree in the spring window. Washed out all the existing soil, and cut back the roots. Planted in a new pot with better drainage (i.e nr of holes) and in pure akadama.
Moved the tree in a spot with indirect sun, and some shade in the afternoon.
I removed all the leaves that looked affected (including new budding leaves, that had black spots). I basically had to do a full defoliation on a weak tree.
Besides this I applied 3-4 treatments of a Mancozeb based fungicide(in cycle of 10 days)
I only watered the tree when the soil would be dry (this would be every 2-3 days). I now water almost daily, as the summer is hot.
As a result, the tree has budded out and leafed out beautifully, and I see no fungus signs.
I still apply a spray of fungicide every month. just to be sure 
Here are some pics:
Sick tree in May (post potting)
Healthy looking tree in July:
