Rotation in the vertical direction is something the Scenery Editor simply can not do. It is,
however, accomplishable by using Notepad.
Before you begin the process you must make sure that everything you want rotated is in its own child scenery (pink box).
Select the child scenery you want rotated vertically.
Export it as a .pc2 file. (File > Export > Current Item)
Delete the item from the original scenery and save.
Close and reopen Scenedit. This clears the default save name. (Not doing it can cause you to accidentally overwrite your original scenery file.)
Create a new map and import your .pc2. (File > Import > Map)
Place it, then rotate it horizontally by the amount you want it rotated vertically. If you want it to be straight up and down, rotate it 90°.
Watch out for positive or negative angles. Generally you want to rotate it positively, and it can get inverted if you mess it up...
Save the current scenery as a different file than your original scenery.
Open the new .fld in Notepad. You will see something like this:
POS -300.00 -0.00 100.00 0.00 16384.00 -0.00
Indicates it's a child scenery.
Tells the program which of the sections above it in the file to look at.
Position in meters. Horizontal, vertical, horizontal. Yaw angle (standard rotate). Pitch (The one you want to change it to). Roll (Used if pitch is rotating it about the wrong axis).
Not a clue.
Ends the .pc2 segment.
You want to move the value from yaw to either pitch (normally what works for me) or roll.
Save the Notepad file, and open it in Scenedit to make sure you did it right.
Open the original scenery, and import the new scenery. (File > Import > Scenery)
Move and rotate the new scenery, now inside the original scenery, around normally if necessary. (Edit > Move > Current Scenery)