I have made some good progress to clean up most of the auto folds in the orginal post. One major issue is keeping an on face inference for the windows especially when trying to array across a large surface. Also the material browser is reporting four faces in some cases=> not good. If I get any thing close to useable will send this pm, XMAS shop time now.
Make sure you understand and use the su inference engine so things are keep planar etc. it maybe the program for the skin gives su some inference poblems. Make sure you lock the on face inference