As for the "holes" - in order to see if your model has flipped face normals, enable Backface Culling in Mayas viewport. (its somewhere under the viewport shading options I think, not up in the menu bar) It will make a polygon invisible if you're looking at it from "behind", while the default option will let you see it from both sides. Then you can select it and use normals>reverse normals to put its normals back to how they should be.
Also I think the AMfP tools will be compatible with the old files. They'd sabotage their own workflow if they weren't, right?