Hi Western, I've got the same result than you.
I haven't found a way to change Y-up before importing the file, seems it is predetermined.
Check Maps properties in the imported materials. Find alpha source parameter for the PNG's wich is set by default to RGB intensity and change it to None(opaque) otherwise model look too bright and shiny, and colors look like too pale, and unrealistic.
To fix the orientation:
--If there is a __ROOT__ object in the scene, or similar, to wich all the other objects are linked, just select __ROOT__ object and rotate with Angle Snap on (A shortcut) in 90 degrees steps, -or 10 degrees if it's more easy- till it faces the orientation you want. (you can set the rotation steps clicking with right mouse button in the icon for Angles snap)
All linked objects will follow the rotation.
--If there is not a __ROOT__ object in the scene file, what I do Is create a helper point object, select all the other objects in the scene and link them to the helper.
Then I rotate the helper to face the correct orientation for the axis. For me it works best to have nose of plane pointing along X-axis, left wing would be along Y axis, like IL-2 world.
I use Maraz exporter and I've also found recently that with previously Buggy Buggy exported models that have top node in the hierarchy with different local pivot orientation, the exported parts come out with wrong lighting, so it may be necessary to re-export again all the parts with new Maraz orientation, (and rebuild completely new hier.him) but I'm still finding out if that's really true, I still have to do more tests...