If you just had planar holes you could do CAP:
This hole is four-sided so networksrf or edgesrf can fill it. The same is true of the one opposite it.
This hole is a more problematic:
Your best bet would be to do whatever you did on the opposite side and not create the triangular opening.
In the alternative, you need to draw a curve to create a planar opening at the top and use planarsrf.
For the triangular opening, you might get away with edgesrf or networksrf. However, you’d be better of making that a four-sided opening if you can before filling it.