I just completed my build and I had a couple suggestions to further reduce the cost by ~$10 or $15. Instead of buying a sainsmart UNO, I bought a Nano from tinkerVault for $10.99 on Amazon. It's tiny and tinkerVault sells it without headers attached. Then I just desoldered the header from the relay board (pull the black plastic part of the header off with a screwdriver first, and then it's easy to desolder 1 pin at a time). That let me easily solder the connections to the relay board and the Nano. Other sellers charge a buck or two more for the Nano but some of them come with female-female cables, which you could use to non-permanently connect the relay board if you want. It appears that the other sellers solder the male header onto the Nano.
I use a raspberry pi and the only change I made was to change the port to ttyUSB0 and ttyUSB1 as detailed in the first section of this page:
http://docs.brewpi.com/after-install/program-arduino.html#troubleshooting
I used the UNO hex and just selected ATmega32 from the dropdown menu in the web interface when uploading the hex to the arduino.
The other suggestion I would make to save money: If you're making your own probes by soldering wires on a bare DS18B20, instead of buying the $12 thermowell from brewershardware buy the $4.75 12-inch straight protection tube. It's thinner so the premade sensor won't fit, but if you're making your own it'll save you $8, and the thinner sensor will respond faster to temperature changes (not sure this matters for this application). I use old ethernet cables and then you can use cat5 ports to connect everything up if you want. I pretty much follow this guide to make mine:
https://www.homebrewtalk.com/f51/make-your-own-precision-ss-temperature-probe-101192/