Hello Dan,
To answer your question, yes, you can use trial and error to guess at the details but it can also be figured. Here's what I've learned after getting help from this board.
First, you start with your magnet disc (rotor)I think you mistakenly called this the stator. If so then you have a 12.25 inch metal disc on which to mount your magnets. You ask about which shape magnet is best. That depends on how you look at it. If you compare magnets with all things being equal then wedge magnets may give the best output. However, they are often more expensive so if cost is the comparative factor then for the cost of a wedge magnet you may get a much stronger round or rectangle magnet. For this reason, 1" x 2" x 1/2" neo magnets are the most common (bang for your buck). You say you are planning magnets so I assume you do not have them yet.
Now putting 12 of these on a 12.25" steel disc will give you a spacing of 1.16" between magnets measured at the inner most point of the magnets. A rule of thumb is to space the magnets with the distance between them about the same as their width so with a magnet 1" wide you would be close. Also, if you want the magnets closer together, just move them in some. They don't have to be right at the edge of the disc.
Now, given the details of your magnet disc you can layout the coils for your stator. Starting with a 12.25" magnet rotor and subtracting 4" (the sum of 2 - 2" long magnets) gives you a diameter of 8.25" measured at the bottom of the magnets. Take the 8.25 x pi (3.14) gives you 25.905" circumference. Now divide that by the number of coils (9) gives you a space of about 2.89" into which you fit the coil. Now subtract the width of the magnet, 1", from the coil width gives you 1.89 inches. Divide that in half and you have about .945" which is the width 1 "leg" of the coil can be.
Next, to figure number of turns, set up your magnet rotor(s) The space between magnet faces, or magnet face to second blank rotor (air gap) can be close to the total thickness of the magnet(s). So if you are using two rotors, each with 1/2" thick magnets, then the air gap can be somewhere around 1". If you have 1/2" magnets on only 1 disc with a second blank steel disc then the gap should be more like 1/2" or to be practical about 5/8". Once you have the magnet rotors assembled you can wind a test coil using any number of turns of magnet wire. The inside of the coil being the same size as the outside of the magnet. Place the coil between the two rotors and alighned with the magnets and spin the rotors at the rpm where you want the mill to start charging the batteries. Measure the output of the coil (AC). If the coil has 100 turns and is putting out 2 volts then you know you have .02 volts per coil turn. Using the output of the test coil calculate how many turns you need to reach about 1.75 to 1.8 volts per coil (for 9 coils, 3 phase). If your coil puts out 1.75 volts AC at the desired cut in rpm the you can use the formula 1.75 volts x number of coils per phase (3) = 5.25 volts AC x 1.7 (3 phase star wired) = 8.925 volts AC x 1.4 (rectified to DC = 12.5 volts Approx. cut in depending on the charge of the battery.
NOW, you know the number of turns, you know how much room you have (thickness) for the stator (coils), you know how much width you have for 1 coil leg so now you can figure what gauge wire will fit. If you are planning a 5/8" air gap then subtract 1/16 each side mechanical clearance, another 1/16 each side for fiberglass mat and imperfections in the stator mold and that leaves you with about 3/8" for the actual coil thickness. Above we figured about .945 for the width of 1 coil leg so the cross sectional area of a coil leg is .945 x 3/8 or .945 x .375 = .355 sq. inches. The amount of copper that will fit in that area is about 60% allowing for air spaces so .355 x .6 = .213 sq. in. Finally, divide that figure by the number of turns your using and using the area of the different wire sizes, see what the largest size wire is that will fit in there. And that's how to figure wire gauge.
Wow, that was a lot of ciphering. I just hope teacher, I mean Flux, doesn't say I screwed up.