Hey,

I have never really imported other models or used blender but here is what I learned from school about rigging and using bones.

You should never scale your bones it messes with there internal orientation.

Also from the sound of it, it sounded as if you were taking the skelleton from a different model that had animation of it already and trying to put it on your existing model. This would be difficult to do as the reasons stated above.

You also mentioned rotating some orients after you have bound your object and at this you are at a wall swing that when you bind your object to the model it is bound. You may be able to unhindered it but I have never had any success with that.

My advice to you is to recreate your on skeleton. And rig it custom to your model and animate it.
Yes I know it's lots of work to do but I have found when it comes to rigging there are no shortcuts. Either do it right, make sure everything is correct or you will ending up doing it again and again.

I learned that the hard way.

I hope others have better more specific advice but from my experience it sounds like what you want to do wont work because the orientations and scale numbers were men's for a different model.