Matthew,
Great thread! A word of advice on the sliding glass doors and that window you mentioned...it will eat floor space and lumber (not trying to spend your cash
), but if possible, build a double-thick stud wall and offset one wall with the other. Often, you will see them at acute angles where the area where the doors open and closes is the tight part of the angle and it widens out from there. Use the big void in the other part of the wedge-wall for heavy trapping (for you that looks like maybe only 18" or so, but you can still load it with 703 top to bottom and cover it with fabric.
On the windows, I bought some replacement vinyl frame double-pane sashes from a window suppier for like $20 each. If you can buy two of the same size (four panes in all), make sure you shift both at angles in the wall (a furred out or 2x6 wall is a big help) creating a "V" if you will. Pain to trim out, but worth it.
Can't wait to see more pics.