"1) From my understanding I can make the design based on what I want my cut-in RPM to be. I found some data and the average wind speed here is 5-6 meters per second. When calculating my cut-in RPM, should I use the average speed for my wind velocity or something else."
Something else. You need to be cut in at something like 3m/s to get power in light winds.
"Also, I need to know the tip-speed ratio to calculate the cut-in RPM. I wasn't a part of designing the blades, but it is a three blade system. How can I go about determining the tip-speed ratio?"
Ask the person who designed it! 3 blades could have a tsr of somewhere between 4 and 8.
If you can't get at it that way then try putting some of your blade dimensions into one of the many blade calculators. That should give you some general figure.
"I have tried using Faraday's law to calculate the number of turns, but for the area term, do I use the area of one magnet, or total area of all magnets?"
Depends on the formula you use. Some use flux per pole and some use total flux which would include total magnet area.
You will find various formulae here and if they are any use they will specify which you need to use. If not don't use them.
I work from flux per pole but my strange equations use frequency which you have to determine from speed and number of poles. Many formulae will give the answer directly from number of magnets.
For what it's worth this is my method.
Volts per phase are given by 4.4x flux per pole x f x N
N is number of turns per phase ( 3 times coil turns in your case).
Flux per pole is gap flux density x area of magnet.
Your gap density will be dependent on the distance between magnets ( stator thickness + clearances). Typically it might be half of your Br figure say 7000 gauss.
Having got the volts per phase your line voltage will be 1.7 x this and the dc figure will be x 1.4.
You will probably find it far easier to look for a formula from someone else ( preferably Hugh Piggot or someone you can trust) and work from that.
Unless you know your gap flux density you will have to make an inspired guess or resort to a test coil like most other people.
For a 12v machine you will have quite a small number of turns and it will need lots of strands in hand, the wire you come up with will be too thick to use directly as it will have eddy current problems if you can handle it.
If you look at the Otherpower 10ft machine with rectangular magnets you will probably find your turns are very similar unless the blade designer has gone crazy.
If you take the 24v coil figures you will need half the turns and twice as many wires in parallel.
I think you would do better to jerry connect it or wind in 3 separate star circuits. Either method will need lots of rectifiers and you may find it easier to mount them up the tower. I really think you will struggle with a star winding with 3 coils in series.
Flux