Bundle adjustment makes the cameras more self-consistent, so rays emanating from matching points intersect better. You can start with no bundle adjustment at all as it may not be necessary.
pc_align is used to bring your DEM closer to a reference DEM. With or without bundle adjustment.
Mapprojection helps when you have very steep areas and you see obviously unresolved regions. On terrain which is not too steep and camera perspectives are not too different, it may not be necessary.
The order, if you use all of them, is bundle_adjust, mapproject, stereo, pc_align.
I will suggest experimenting on small clips, as this can greatly reduce the amount of time for trying things out. The stereo_gui program, the ISIS crop command, and the gdal_translate tools can create crops (for various purposes).