You should not change the object's transform(aka pivot point) to move/rotate/scale.
You want to use a "working pivot" or a temporary pivot to move/rotate/scale your object from different points so that the object gets translated, but the object's pivot actually doesn't get modified when you do it, the object pivot should be at the center of the mesh and have its original orientation.
For exporting to game engines, generally and specifically on this case, since we are dealing with collision boxes, you want the object's pivot to be at the center of the mesh.
Here's some examples, box just created, its local transform and global transform look like this:
If I move, rotate or scale the object, its local transform still is centered and orientaded as it original was, and should be!
Global transform now looks like this (global transforms are orientated relative to the world transform)
Here's a quick video that explains working pivot, I don't use 3Ds max, so not sure if there are faster tools to do this:
http://www.youtube.com/watch?v=M6SHIKIDOPU
As for exporting the position and rotation data, it should be easy as long as you have exported each box that has a different scale as an individual "bloc" (+coll + phmo etc).
Normally, it would be better to have every different box placed at the origin of the scene for exporting as the base objects for the coll/phmo and visual model, but given how you are building boxes over your level directly and then wanting to export placed boxes, you can still do it, it just requires a bit more programming.
You can either write a mesh exporter to do this, or you can also more easily freeze the object scale tranform so that its scale is applied to the mesh and 3DS max should take care of exporting the data properly for you, there should be export options to choose if you want to export the meshes as individual objects and in global or local space as well as the transform order (XYZ).
But if you want to write a mesh exporter, 3DS max should have a scripting/programming API with all the math and functions to the local/global space conversions, and most likely the mesh components can be read in local and global space already.
You want to export the vertex position relative to the local space (its transform that should be at the center of the mesh, and properly rotation aligned to the box-mesh (0,0,0)) for mesh data.
As for exporting the position and rotation data for spawning the bloc item, you want to export the pos/rot relative to Global space (global pivot/transform).
This is assuming you kept the box pivot at its center and properly oriented, as it should be went you created the box.