I populated one of the temperature controller boards, did some testing and then loaded the PID software and tried out the IR sensor. So far, everything seems to be working. I don't have any of the thermocouple chips to try out so that will have to await the next parts order. But so far, so good. I'll be happy to help anyone get their board built out and running.
Edit- After checking some more, there is one thing to be aware of when building the board. It has to do with power from the programming headers. There are two different programming headers on the temp controller board. One is a standard 6 pin AVR ISP programming header. Most AVR programmers that I'm aware of have a provision for dealing with powered or unpowered target boards. There is usually a switch (or jumper, etc) to select whether or not the programmer will supply power to the target board. Since the temperature controller board is designed to be powered when it is programmed, you should set your AVR programmer to *not* supply power.
The second programming header is a standard Dorkboard 5 pin header. The middle pin of that header supplies 5VDC. However, there is no provision to select whether or not that pin is powered (it always is). So if you use a Benito, for example, to program your temperature controller board, you will have 5VDC coming in from the Dorkboard connector in addition to the 5VDC and 3.3VDC from the regulators onboard the temperature controller. This probably won't do anything bad but it would be better to avoid it. The simplest way to fix this is to not connect the middle pin on the Dorkboard header. If you populate that header to be compatible with a standard Dorkboard layout, you will put a female header in that position. So just pull the middle pin out of the female header before soldering it onto the temperature controller board and then the 5VDC will never be connected from the Dorkboard programming header. That way, there will never be 5VDC coming in from more than one source. On the next version of the board, I will probably not connect the 5VDC pin from the Dorkboard connector to avoid this issue.
If this isn't clear, just ask me.