Note that this is now a dated installation. As of November, 2011 I'm using two probes permanently installed in the rear wall of the roaster, using instructions on this page.
One of the challenges of getting consistent and useful data is how and where to place the thermocouple. One of the primary advantages of using a thermocouple is that you can get it into the bean mass and get temperature readings from the outsides of the beans. Pair that with the air temp just above the bean mass, which is where the built-in probe reads on the HotTop, and you have usable data.
For the most part, I followed the guidance of Espresso! My Espresso! with a few changes. First, double-check his measurements — they didn't work for me. Second, I was in a bit of a hurry and had a couple glasses of wine (shocker), so I ended up placing my probe on the opposite side of the chute cover. The probe still reaches the bean mass, just not as much as it would on the other side and it's closer to the heating element now, possibly influencing the temp.
At any rate, I used the same probe he recommends; the Omega KTSS-HH. I bought a replacement chute cover so that if I destroyed it, I destroyed a spare, and I used a 9/64" cobalt drill bit and my ever-handy Dremel to cut the long opening and also to smooth down edge. One idea is to use JB Weld to secure the probe and seal the gap, something I'll try soon. More on that later.
Now, with the thermocouple mounted in the bean chute cover, my temperature readings are consistent and I don't waste the first five minutes of the roast futzing with the probe trying to get it in the bean mass and not wrapping around the drum shaft. My first probe was the exposed-tip wire K-type probe, which I did manage to get wrapped around the drum shaft once and had to eject the beans to retrieve the probe.
Be careful how deep you place the probe. This probe is long enough to extend far enough into the drum to obstruct the fins, which could at a minimum result in a bent probe or it could damage the HotTop motor.
I left 1" of exposed metal sticking out of the chute cover.
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