If anyone's looking to roll your own reflow oven, Kevin Darrah had a couple of nice videos on it.
He, like Mike, left the time enabled and also left the internal thermal protection enabled in case the microcontroller goes into a runaway mode. That way the oven will turn off by itself and at least won't go over the maximum safe temperature for the oven. Also he found that he could get a lot better temp control by coating the glass with foil. He also mounted a small fan in the back to circulate the air to help eliminate hot/cold spots but my concern with that would be even with the fan on a standoff, it could start to melt.
One thought I had is you could also do it without modifying the oven at all. Just move the electronics into an outlet strip or use a Power Switch Tail that is controlled by your Arduino.
The actual setup he had was, Arduino (well AVR board programmed as an Aduino), cheap Walmart oven, Sharp 16A/250VAC solid state relay with heatsink, a start button, K type thermocouple, Maxim thermocouple amplifier, and a standard Hitachi interface 2 line LCD.
Video 1 is the teardown and conceptualizing of the design, Video 2 is his finished design and explanation of what he came up with.