Laeyto, evidently you are aware of what may have been factors and what may help. And certainly you are going about this both the right way and very well. Keep up that reading.
I note Formula from day one and Antibiotics . For me these are probably the biggest concerns. Getting as complex a gut flora as possible is what is now required. Doing so will not be easy. But it can be done. The issue is how to progressively build that gut biota. My guess would be that the "Ultra Flora" you mentioned was too much at this stage. Starting "small" and cautiously after the fast would be wise.
Let us know how you get on. That will give us a much better way of advising you rather than just punching in the dark.