Mind you some of the pictures are hard to tell alot of detail. Tried blowing them up looses detail. It appears some of your headers are not doubled and you do not have jack studs under them. Your flashing appears to be installed wrong under the windows however its hard to tell. Did you ptu you bottom flashing on befor you installed the windows? Yout house wrap did you x and fold in at the windows? Then did you v up the wrap at the top of the windows put your flashing on after the window was installed then fold the wrap back over the flashing and tape the cuts? How long do they allow you to have untreated wood exposed to the weather before covering?
Again remember its hard to see all detail, and you do have codes that may differ some from N.C. to where you live. Also you may have already taken care of some of these concerns since you have taken these pictures.
Also you have done well considering you had to take so long off. It may have been advisable to have had some help to get your project dried in sooner. However I like you like to do things myself and sometimes its to my detriment also.
On you building where you have the jalousie windows did you install top plates? Also on all your rooms did you install double top plates. Again you didnt show all walls after completion. Pictures can be hard to go by.
Hang in there and work with your inspector, Im sure he will help you if any of these are any of his concerns. Remember he is a public servant. I hope he works well with you.