Filling in a "hole" on a 3D Model

Hi all,
I'm currently working on a Palazolli plug and I think I'm coming along decently.

the plug features an angled cylindrical shape through it as well as 2 triangles for mounting a hinge. my issue can be seen in between the 2 triangles.
I have managed to somehow delete a portion of the object, and I don't know what shape or command to use.

In the attached file you will find my design. the "hole" is ellipse shaped.

(Bonus: The inside of the cylinder, as you will see, is quite.... messy. would there be any way to clean this up?)

Thanks community!