If I replace the stock fan in my Xbox 360 with something quieter, would my console be flagged as 'modded' and hence ban my console, or live account?
I have heard of this happening to some people. Apparently, the fan causes a greater (or perhaps fluctuating) voltage drop which the console detects and reports back to Microsoft. This can apparently earn you a ban, possibly because mods can cause the same sort of effect.
Instead of replacing your existing fan, can you use an externally powered or USB fan to blow extra air in? I can't remember if the 360's fan is temperature sensing but that might cause it to run slower.