The new roof will wrap up this wall and get terminated a foot high with the bar.

Roof flashing at the wall is essential. This can cause roof leaks!

This roofing system needs to be replaced.  There are too many problems to repair.  The easiest solution will be to:

overlay 1.5-inch iso boards and screw them down.

Screw down mechanically and fasten the TPO membrane on top of the roof.

The new membrane will fix these roof penetrations.