I am having the hardest time figuring out how to drill through these 2 holes where these two parts meet. How can I do this off plane? These holes need to be aligned and perpendicular to the part so the screws can fit.
Welcome to the forum.
If I understand correctly and you deleted the sketch, just double tap the flat part with the holes to enter Sketch mode, draw two new circles the size of holes you want. Exit Sketch mode, tap inside the circles and extrude them into the body to make new holes.