The arduino will then communicate with a computer and send an email out notifying me of which sensor tripped.

You don't need a computer to send an email from your Arduino. An ethernet shield would suffice.

Can you access the server 54.245.100.105 from your browser? (I couldn't)

Connections to the display are as follow (copied from the code):

Code:

#define HT1632_DATA     6    // Data pin (pin 7 of the display)
#define HT1632_WRCLK    7    // Write clock pin (pin 5 of the display)
#define HT1632_CS       8    // Chip Select (1, 2, 3, or 4 of the display, depending on the ON switch)

You can force the position of the tilt in the code, in function loop().
The buttons are on pins A2 and A3. These 2 pins should also have 10k pullup resistors to Vcc.
I think the first thing for you is to get the display working. You could use this (simpler) test program:
http://code.google.com/p/wiseclock2/downloads/detail?name=Test_3208.pde&can=2&q=#makechanges

Since you have a working prototype, why not just experiment with it?
The WiFly module should do well in your empty (no walls) hangar of 35m x 35m (aprox 1,000 square meters).
The battery consumption depends on the software as well. To save the battery, you will need to do http requests (those take 210mA) as rarely as possible.

TopTube,
You connect the DS1307 RTC to your Arduino on I2C, as shown in the datasheet:
http://datasheets.maximintegrated.com/en/ds/DS1307.pdf
SDA and SCL are pins A4 and A5 of your Arduino, respectively.
You need 10k resistors as pullups on these 2 pins. Backup battery is also necessary, as is a 32kHz crystal.

According to this article (at bottom of the page)
http://msdn.microsoft.com/en-us/library/windows/desktop/aa365247(v=vs.85).aspx
try using   \\.\COM16   instead of just COM16.

This is what the error means:
http://support.microsoft.com/kb/276011
Probably your COM16 does not exist. Can you find it listed in Device manager?

If I remove COM7 on my machine, I get the same error 0x800A0035 ("File not found").

As I said, as a syntax test, try COM1 instead of your COM16.

And why do you have COM16? Are you using a Bluetooth USB module?

I tested it on my Win XP machine and it seems to be working fine.

Yes, use your port instead of the COM7 I used as example.
If you get an error ("cannot open" or such), try a "traditional" COM port (e.g. COM1), listed in the hardware profile.
Also, make sure the COM port you use is not already in use, by Hyperterminal, serial monitor or other terminal app.

I modified the above VBscript for you, to send just one character, "1":

Code:

Const ForWriting = 2
Set fso = CreateObject("Scripting.FileSystemObject")
Set com = fso.OpenTextFile("COM7:9600,N,8,1", ForWriting)
MsgBox("Ready to write a character to COM")
com.Write("1")
com.Close()

Also, keep in mind that Bluetooth has a range of only a few meters. A WiFi network can cover an area of tens/hundred meters, depending on your wireless router. WiFi gives you access to the internet, unlike Bluetooth.

Look at the EthernetClient example coming with Arduino IDE. That's closer to want you want to achieve (make an http request, get a response, then parse it).

Maybe "propeller clock" (with POV)?

I dont think anyone would open the CPU to see our programs

Sometimes it is just easier to reproduce the functionality, without necessarily copying the software, black-box style. The new software may work even better than the original.

Each of the 4k7 resistor has one terminal connected to A4/A5 and the other to Vcc.