I've added the latest EAGLE design files for the two controller variants, the power board and a new SMD variant of the power board.
I'm still keeping the files around for a through-hole power board variant, as it solves the bootstrap problem. To build your very first reflow oven, you can use the through-hole power board, modify the oven, and then use an Arduino Uno and a thermocouple amplifier breakout board and jumpers as your first controller. Once you have that working, you can reflow an SMD controller and switch over to that.
To make an Arduino Uno based reflow controller, buy an Uno, an AdaFruit i2c 2x16 LCD shield and an AdaFruit MAX31855 breakout board. SparkFun has a similar breakout board, but the AdaFruit one has a 3.3v LDO and level shifters so that it's 5v tolerant.
Connect the breakout board ground to the Uno ground, Vin to 5V, !CS to D7, SCK to D13, DO to D12. Connect D2 and D3 to 150Ω resistors in series with the element lines for the oven. Connect a K thermocouple to the breakout board and route it somewhere convenient inside the oven.
With that done, grab the i2c display version of the sketch from the GitHub repository. You will need the Arduino PID library and the LiquidTWI2 library to control the display. Upload that code into the Uno.