You should be able to select the mesh, go into Object Mode, click on the "Object" tab and open up the "Transform Properties" box. Alternatively, you can bring up the Transform Properties by hitting "N" on your keyboard.
Take a look at the Loc X/Y/Z and Rot X/Y/Z values. They should all be 0.000. If they're not, then you should be able to set them back to 0.000.
As a side note, the only thing necessary to make replacement animations is the exported skeleton. So even if the model is a little distorted, it's only there as a guide on what the animations will look like.
Of course, you'll have to keep in mind that your model is a bit off axis when animating with it, but other than that, I think you should be alright with it.