You can use Rotate Object tool for unrefrenced chunks to change their orientation in the coordinate system.
shown in the attached image, it does do what you want it to do!
My preferred method of using it is:
1. hit numpad 7 to go to top view
2. then invoke the rotate object tool to rotate the model to a top view.
3. hit space bar to return to 'normal' navigation mode
4. hit numpad 1 to go to front view
5. hit space again to return to rotate object mode and fine tune the rotation in front view
6. hit space to return to normal nav mode again
7. hit numpad 3 to get a side view
8. hit space to get back to rotate object mode and further fine tune the rotation if required
9. hit space to get back to normal navigation mode
10. hit numpad 7, 1 and 3 in sequence to check the model is aligned and repeat the above if necessary.