Hello Thijs,
Maybe you can specify the settings that you are using on every processing step?
To reduce the alignment time you can use lower point limit (20000 for key points and 4000 for tie points), use preselection (Reference is preferred providing that camera center coordinates are available).
For dense cloud generation speed up we suggest to use 1-2 graphic cards like GTX 980 Ti, GTX TITAN Z, or Radeon R9 290x, for example.