You said you didn't know how to fix the orientation so I figured I'd let you know. It's pretty straight forward. First add a coordinate system via Reference Geometry -> Coordinate system. If the model is in the correct printing orientation when you're looking at it in the default isometric view (ctrl+7) you would click in the Z-axis box and then select the top layer as the reference and hit ok. If it's in some other orientation you'd have to change that accordingly.
Now as you go to save as STL you click the Options-button in the save dialog and change the Output coordinate system at the bottom to the one you just created.
And if I may give a small piece of advice for the design it is to give all the platform facing faces a chamfer of 0.5-1mm, it makes a huge difference in print quality IMHO. It helps get rid of the elephant's foot and makes parts fit together much better (especially nice with meshing gears for example). It can also help if you want a fillet towards the platform. See example here: http://support.3dverkstan.se/article/30-getting-better-prints#chamfers