Hi, Pete,
just in case you find it helpful, there is something you can do when you need to rotate a whole object made of many parts, or a bunch of them or the whole scene (or a set of plans). That is, if you don't mind to remake the hierarchy, if you have one.
-Just create a point helper and place it at the center of the scene (0,0,0)
-unhide all the objects you need to rotate (usually you can go with "unhide all" if it's the whole scene) and select all of them.
-unselect only the point helper you made and use select and link tool to link all objects to the point helper.
-select rotate tool and change "reference coordinate system" to "World", also change "use center" flyout to show "use transform coordinate center".
-now rotate the point helper the amount of degrees you need. (you can use "Snap angle" to make it easy)
All objects linked will follow and rotate the same amount.
Be sure to delete the point helper when you are done and restore the hierarchy of the parts if you previously have one.
This also works for moving or scaling.
I've had to do this for all the scenes when I shifted to Maraz exporter and 3dsMax 2012, as I was following modelling bible convention of building models along the Y axe.
At least for me, and I recommend it, is much better building along the X axe instead, and make things a lot easier as you will have the same orientation in your scene as in IL-2 once exported (Maraz).
Probably you already know, but be sure to reset Xform before exporting, from time to time you will see some part turning outside out in your scene after that, (that black color in the fuselage in your screenshots is a good hint) so you will need to flip the normals before export, as you have done already.
For some other more tricky parts, usually the ones that has been linked to another one wich has been scaled, you also will need to reset their scale. You will find a button for that, inside the pivot tab.
Their size will be gigantic or very tiny once exported and if you look to the attaching section in the him.file, you will see their matrix definition starting with some odd numbers.
Glad you keep with it, and congratulations! being able to see your previously non existent meshes in the sim, is maybe a small step, but tastes like a great victory...