First I'd check for corroded leads. When you're in that low a voltage range, it doesn't take much to futz up the works. Hopefully that's the problem, since it takes about two seconds and a knife or fingernail file to fix.
Set your MM to millivolts. With the pilot light on and switch off, the thermopile should be generating at least >250-350 millivolts, if it isn't, it's probably bad. When you flip the switch to turn the burners on, it should drop by about half. If it drops to zero or close to zero, it's got a short. If it doesn't drop at all, the problem might be in your switch.
With it set to ohms, stick the leads on either side of the thermistor, then turn on your pilot light. You should either see the resistance start to increase or decrease, depending on what kind it is. If it doesn't, it's probably bad. If it reads infinity, it's definitely bad.
I'm used to dealing with them from ovens and dryers and the like, not heaters, so take all that with a grain of salt. 
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