From the picture and your description, you have a solid hole. Flo Sim works around solids by adding fluid in the 'empty areas'.
Make a large solid, then use Cut/Extrude to cut a hole in the solid. Add two lids on either end of the hole, with the drill inside of the empty hole. Then add a Fluid Domain by selecting the inside surface of one of the lids.
A solid hole won't work, but a hole in a solid will work.
Felix, do you have any boundary conditions applied yet? What type of analysis are you planning on running? Internal? Where will the boundary conditions be applied? Will you be including cavities without flow conditions?
If you save your assembly as a part, are you able to merge the bodies all together? If you draw a huge solid cube overtop of all the components are you able to use combine subtract to remove your assembly bodies from the cube? If you can't do this, Flow Simulation won't be able to either which is the equivalent to the fluid geometry failing to be generated.
Based on the error message, my guess is that the interferences are causing trouble. Try using the cavity feature to trim one component with another and see if that helps.