hey sgt
The most likely reason your normals appear to be flipping is even with two sided lighting on if you have scaled anything in -1 then they will still appear fine in maya. When you export them to obj they wiell then be "frozen" which effectively sets the scale to 1 and flips the normals.
So to see and fix flipped normals before going to obj select all the objects in your model and freeze their transforms. This will flip any -1 scaled components and they will turn black with show two sided lighting unchecked.
No one has come up with the "magic-make-my-model-all-clean-quads" command yet. If they did they should win a Nobel prize. So if you must have clean quads you will need to work on creating them as you go.
If however, you do not need to smooth your model you can use mesh > traingulate to make it all tri's. However, if the goal is to go to obj to rhino and then obj back to maya and then smooth you'll have a mess.
If your goal is to make water tight models for stl (stereo lithography or 3d printing) you can have all the n-gon and tri's you like so simply boolean the crap out of it and then triangulate the mesh.
I work with someone that makes molds for models and his meshes are horrific but they convert to stl files just fine and he does not get paid for how clean his mesh is, he paid for how many meshes he turns into molds; so spending hours cleaning a mesh that does not require it is just wasted time. The only time you'll have a real problem is if the surface with the ngons becomes non-planar then you will get uneven artifacts and the you will have to clean the edges and shoot for clean even quads or tri's.
update:
I was looking at your mesh images and I did see one thing that is very bad for stl and that is any face with a hole that does not connect to an outer edge. See the attached image. The one on the left is bad, very bad, because you have a hole inside a poly face with no edges connecting to the outer edges.
The second version is better as there is an edge connecting the inner hole to the outer edge of the face the hole is in. You actually only need one edge and you see this in 3ds models all the time. You have two very obvious ngons but for STL they DO NOT MATTER. The face is planar so there will be no artifacts!
The third I have taken a minute or two to make quads. So now the model is all quads but for STL the results of this mesh will be no different then the mesh to the left. So the time to quadrangulate really did achieve anything.
Now please before I get all kinds of hate messages. This only applies if you only need a water tight model, do not need to smooth, do not intend to texture (you have uneven uv spacing so you would want even vertex distribution).
"If I have seen further it is by standing on the shoulders of giants." Sir Isaac Newton, 1675
Last edited by ctbram; 12-10-2012 at 03:03 PM.