Your pic shows a rather poor connection between the pipes and the floor above, at least in the bits we can see - air is a reasonable insulator so as things stand you are not getting the heat from the pipe into the floor very well, can you still access it or are you beyond that stage already?
Going forward there are perhaps two approaches.
Try to stop all flow in the downstairs and then experiment with the upstairs manifold flow rates and the water temperature (+delta T) to see if the upstairs system can be adjusted to cope without the downstairs in circuit. (Keep notes of the present settings so you can return to them at any point.) If it can't then you may need to fall back on making the downstairs do all the work.
Do the heat calcs - how much heat you need out of each zone for the length & diameter of pipe, coupling losses, area of the zone etc. Then adjust the flow rate settings in the controller for each zone and see what happens.
I get the sense from your original post that the bathroom is your principle concern so maybe just run / play with that loop. Get a gun type thermometer to measure the temperatures everywhere (pipes, floors etc).