DPR, I know I will get some fire for my response and it will certainly not help at all,
but I have yet to see a lossless FSDS2Gmax conversion.
For me it's not worth the hassle.
My suggestion is, scrap FSDS entirely and stay in Gmax all the way as it's lightyears ahead in it's capabilities.
I was thinking to suggest this when I saw your firsrt picks of your cockpit cutaway.
You can do that much better in Gmax using a boolean operation rather than going the quite annoying delete_poly_and_move_point box-modelling technic that FSDS can offer.
you have many more tools for instance to keep your symmetry, to avoid these smoothing errors in the cutaway in first place, errors which are typical for many FSDS designs btw.
Check out the tutorials section and forum over at
http://www.freeflightdesign.com/Lot of great info and helpfull people over there.