Good news - I just figured out how you can safely get your object into the proper rotation in MilkSjhape - it makes all the editing MUCH easier

Here's how:

As soon as you import your .obj file for the first time, do this:

1} On the menu, choose "Edit/Select All"
2} Click the [Rotate] button
3) Type in the "z" section 90 in place of the 0
4) Click the [Rotate] button that is right beside it
5) Leave "z" at 90, and type 90 into the "y" section as well
6) Click [Rotate] again - your object will now be facing correctly, the Front Window will show the front, etc.

Now do all your editing, texture mapping, and all the rest - you can save as a .ms3d file whenever you like.

But, at the very end, when you are all finished and ready to export the final .obj file:

Make sure ALL your groups are showing by using "Edit/Unhaide All"
Then "Edit/Select All"

1) Go to Rotate again.
2) Set x = 0, y = 0, and z = -90
3) Click [Rotate]
4) Set x = 0, y = -90, z = -90
5) Click [Rotate]

Now your mesh is back in that same awkward position the way it came in, and it is safe to Export it to an .obj file to put back in your game.