There are 4 fans:
1) Attached to the back of the tower is the now not-working ~3x3" fan
2) The sound card GPU has a working fan (attached to the GPU)
3) The motherboard CPU has a working fan (attached to the CPU)
4) The power supply has its own working fan also (inside the power supply)

When I added a few disks and cleaned out the dust inside, I disconnected
all the SATA power cables and bought af Molex-to-SATA adapter, where, when
I put it all back together and powered it up, the main #1 fan above isn't
working anymore.
http://img4.imagetitan.com/img.php?image=17_fan.jpg

I've been using the computer for a few days without that main fan.
Googling for how to check the temperature, I installed and ran Speedfan.Exe
with the side cover removed.
http://img4.imagetitan.com/img.php?image=17_clipboard015.jpg
I think the only tab in Speedfan.Exe that is useful is "Readings".
- Fan1: 0 RPM, Fan2: 1236 RPM, Fan3: 0 RPM, Fan4: 0 RPM, Fan5: 0 RPM
- GPU: 73C, Temp1: 45C, Temp2: 29C, Temp3: -2C, Temp: 0C
- HD1: 43C, HD2 44C, HD0: 40C
- Core 0: 37C

The only thing I see 'wrong' perhaps is that the graphics card has a 6-inch
set of black and white twisted wires that aren't connected to anything on
one end as shown below.
http://img4.imagetitan.com/img.php?image=17_computer_1.jpg

I don't remember if that set of wires was connected or not, so I left it
unconnected. Plus, why would a graphics card control the "main" fan anyway?
http://img4.imagetitan.com/img.php?image=17_computer_2.jpg

The motherboard & graphics according to CPU-Z from cpuid.com a
- Gigabyte Technology Co. Ltd., Model EP43-UD3L
- Nvidia GeForce 8500 GT, ASUSTek Computer Inc., G86, Revision A2

The "sensors" reading of the GPU-Z software from TechPowerUp says:
- GPU Temperature 73.0C
- Fan Speed 40%
http://img4.imagetitan.com/img.php?image=17_clipboard0219.jpg

The fan seems to only have two wires going to it which come from a Molex
connector with original pigtails, so the fan has power I'm pretty sure (I
haven't taken it out yet becuase I think the two wires coming off the
graphics card are what caused the fan to stop.

Any advice for what makes the main #1 span spin?
(Could it be the twisted pair of wires coming off the graphics board?)

If the machine runs without the fan, will it shut off when it gets hot?