Found a solution for this.
Edit the main.mcf in the Documents\Aerofly FS2 folder as follows:
Replace
<[list_tmsettings_separate_3d_view][separate_3d_view_list][]
>
With
<[list_tmsettings_separate_3d_view][separate_3d_view_list][]
<[tmsettings_separate_3d_view][element][0]
<[float64][x][0]>
<[float64][y][0]>
<[float64][w][0.325]>
<[float64][h][1]>
<[float64][field_of_view_factor][1]>
<[float64][y_axis_offset_in_degree][-3]>
<[float64][z_axis_offset_in_degree][-90]>
<[bool][is_fixed_default][false]>
<[bool][is_main][false]>
>
<[tmsettings_separate_3d_view][element][1]
<[float64][x][0.325]>
<[float64][y][0]>
<[float64][w][0.35]>
<[float64][h][1]>
<[float64][field_of_view_factor][1]>
<[float64][y_axis_offset_in_degree][0]>
<[float64][z_axis_offset_in_degree][0]>
<[bool][is_fixed_default][false]>
<[bool][is_main][true]>
>
<[tmsettings_separate_3d_view][element][2]
<[float64][x][0.675]>
<[float64][y][0]>
<[float64][w][0.325]>
<[float64][h][1]>
<[float64][field_of_view_factor][1]>
<[float64][y_axis_offset_in_degree][-3]>
<[float64][z_axis_offset_in_degree][90]>
<[bool][is_fixed_default][false]>
<[bool][is_main][false]>
>
The mouse and map will be back but the clickspots are not correct.
Workaround is to rotate the view down so the switch you want to click is more or less in the middle of the screen and click above and below until you find it.
Not great but worth the three screens
>