I have no experience with Revit, however, unless you need the stories for some BIM reason (classifying elements as to belonging to a certain story ID), it is easy enough to draft up a 2D line in the section to act as the story level and to just disable the story markers and use the dimension tool to annotate the elevation/section height dimensions.
It is not easy, however, to go back on your story settings. So make sure you have a backup file, before deleting stories, as this will also remove all elements linked to those stories.
All that said, with floorplan cutplane settings, you can achieve a lot. You can customise per view how far up or down things should be projected and there is ussually an option to 'override', by settings elements to 'home story only', however that will probably not work for most walls and such that will span multiple split levels.
Erwin Edel, Project Lead, Leloup Architecten
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