As others mentioned before, your cards shouldn't really go up to 100 ºC. What GPUs? How are they mounted? Clocks? Miner settings?
Im wondering how much of the heat is related to scrypt rather than SHA256 mining
That depends. Chances are, you won't be able to mine a scrypt-based coin at the same core clock than a SHA256-based coin, but you'll need a higher memory clock and a higher intensity.
Advantage of SHA256: You can underclock the memory to 300 MHz and still get the same hashrate.
Advantage of scrypt: Since the memory clock will be more limiting than the core clock, you can undervolt the GPU (if your card permits it).
Both method can lower the operating temperature dramatically.
what you experiences are with thermal throttling, GPU fan death and heat related component failure
I don't let my GPUs go over 80ºC. I also limit the fan speed; you can't really go by the percentage, since one card's 60% might be another card's 100% (rule of thumb: if it sounds like a jet engine, it's going too fast). So far, none of my equipment failed.
overall the best way to run rigs in the heat.
If you can, build an open case.
Make sure all your fans are clean. Removing the dust from one of the
case fans lowered my temps by 5ºC...
For SHA256, using CGMiner's built-in GPU throttling is straightforward. Specify a target temperature, and it will underclock your GPU if it starts to run too hot. Since clocks for scrypt are deep magic, I'm not sure if automatic clocking is a good idea.