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In my office we would perform all of the procedures at the same time. There is no reason to put you through multiple appointments when one visit is suffice. We would replace the fillings on the molars and following that extract the wisdom tooth. Hope this helps.
You did not mention the reason your dentist wants to remove the wisdom tooth...if you have gross decay or infection, I think that would take precedence or priority over repairing older fillings. If there is nothing wrong with your wisdom tooth, why does he want to extract it? I need more information before I can help you, but I would start with what hurts, or is infected or what has decay. Take good care!
The wisdom tooth only needs to be removed first if it is in the way of proper filling of the adjacent tooth. Otherwise, it can be removed after.
It can take longer than 1 week for the stitches to dissolve.  Don't worry about that.  If you find it uncomfortable, then I would recommend that you call the surgeon that removed your teeth and have him look at the area and remove the suture if necessary. 
Your symptoms are classic for Acute Alveolar Osteitis or "Dry Socket".  Of course without examining you this is only a VERY educated guess.  "Dry Socket" is when you dislodge all or some of the blood clot in an extraction site or the clot breaks down on its own before it matures. This...
I would advise you to go back to the oral surgeon to evaluate for infection or for possible "dry-socket". Both conditions could cause severe pain. It also might be the normal healing process. Let the surgeon decide for sure.