I've now had the new fan speed and temperature-monitoring device in use for about a week and it's all working fine. Disabling those Fan Fail warnings in the BIOS was no problem, it transpired. No sign of any boot-up warning.
The device I'm using is a Scythe Kaze Master II, which slots into a 5.25" frontpanel bay. The Master II is fairly new on the UK market, I think, though Scythe have been producing fan controllers for some years. It has four-channel monitoring and an electro-fluorescent speed-and-temperature display. A nice feature is that each channel's speed control (pot) is retractable, making it flush with the frontpanel when not used. Handy for those with desktop machines that have a door on the front. The only criticism I have of the Kaze Master II is that the display is recessed by 0.5" or so, so you have to stand back, level with it, to see the readings.
I don't push my CPU and generally my thermal requirements aren't tough but using this device has certainly tidied up a lot of my Heath-Robinson alternative controls inside the PC and has now meant that I can finely tailor the speeds of my fans for absolute minimum noise. This can be crucial when tuning for minimum acoustic resonances. Identifying an offending fan is simple - you just turn the frontpanel control to minimum to turn the fan off. The Kaze Master II always gives the fans a kick start when the machine boots up. It has the usual built-in alarm, just in case the CPU temperature runs away, and also a feature for automatically removing the 12v feed to a fan if the fan refuses to turn (preventing burning out of the fan's motor).
Though I've used them, I've mixed feelings about the worth of the temperature sensors, especially since in this context thermocouples are invariably impossible to fit in the ideal places. For the CPU temperature, I'm still going to rely on the figure the BIOS gives me.
Now running inlet and exhaust fans at 630 rpm each and CPU fan at 1000 rpm, the CPU temperature rarely gets above 35 degrees C, as measured by the BIOS. The heatsink temperature, as shown by the Kaze, gets to about 31 degrees C. Inlet and exhaust temperatures are now typically 23 degrees C and 29 degrees C, respectively.
Hope this proves useful to others.