I put together a video on Youtube (unlisted) that demonstrates some of the things you’d like to do. I sort of recreated part of your model and the first thing I did was remove the fillet radii to work with hard surfaces. I left the fillet on the hole purposely just for demo sake.
Double tap on the top surface and it allows you to sketch on that surface. I did an arbitrary offset from the hole just to get its center point. Draw a horizontal line from the center of the hole. Note the center point along the vertical face of the surface. Draw a horizontal line from that center and note the dimensional difference between the two lines. That’s how much you need to offset the hole to get it centered on the surface.
Select the center wall of the hole plus the fillet and use the Move-Rotate tool to move the hole by that measured amount to center the hole on the flat surface.
Use the same technique to rotate the angle of the body where it is stepped to the desired new angle and you can also move the angle portion to whatever desired place you like.
At this point I like to make a duplicate body moved over some distance that is easy to remember like 2" in my example. Hide it for now and use it for reference if needed. Then add the fillets to the first model and proceed to 3D print.
As Istvan stated, this direct modeler is very powerful for modeling but requires a different mindset. Sketches are fine to get you started and once you create bodies it is sometimes easier to manipulate the surfaces instead of going back to the sketch. Sometimes it is easier and makes sense to start over especially if your model has many fillets and compound fillets that cannot be undone.
I hope this helps you out.