Yes, its a complete circle, it is cut to the *inside* diameter of the bio tower, so the bio tower can sit *on top* of it. Also, see page 186 where the lower portion (that's inside) of the box, is a continuation of the bio tower, although its a separate piece
Although you will get better performance with a taller setup your's will be fine. Having the skimmer fit under the tank is always an issue with hobbyists. (but its no problem) You main concern will be draining the contents of the skimmer into the sump.
See page 185. The collection area and upper reactor area are all one piece. That is joined to the lower reaction area as shown in the diagram.
The more overlap the better. Mainly you need the overlap so you have a place of the nylon bolts. The bolts are about 5/16" A one inch overlap is good and keep in mind it does *not* have to be round. Square is easier to deal with and will end up giving you more material when the bolts are tightened.
I would think about 700- 900 GPH, no more than 900. Your main concern is the fact that the skimmer will be below the sump water line so you don't have the advantage of full gravity drain. You will have to empty the skimmer at the same rate water is pumped in.
Thank you very much
not to add to your concerns ;-) but you may find these links helpful http://www.cs.cmu.edu/~cap/pictures/myreef/skimmer/index.html
http://nucalf.physics.fsu.edu/pfohl/Fish/Diy/downdrft.jpg
Also check on the cd under Tanks, Sims Lowry. He did a nice job taking pictures, That will also give you a good visual of work in progress.
If you need any more help feel free to mail me. I understand when a project is underway, getting information is very important. Thanks for your support Robert