When I link a Revit file into another one, the elevations of the linked one are also coming through, but the elevation markers are all over the place, is this because the two files are not lined up? how would you deal with this situation?
For this scenario ideally you would want to utilize shared positioning, in order to align the coordinate systems [including Elevation] between the 2 or more project files. You would choose one of the project files, which you want to utilize the location\elevation data from. Then you would either publish or acquire the coordinates; I have included some resources below on this subject:
Revit – Acquiring and Publishing Coordinates
True Elevation and Position
Shared Positioning: Linking, Recording and Publishing Multiple Revit Site Locations to Linked Project Files