At some point, I'll add a proper writeup here on how to build your own "black box" for the DIY'ers out there. In the meantime, please have a look at Alphaomega's STC-1000+ Project on Github if you'd like to learn more about the firmware and how to flash it onto your STC-1000 (or check out the video below). Also, there are many good writeups out there on how to enclose & wire the STC-1000 controller, here are a few good ones:
Here's a video I made explaining how to flash a controller with the STC-1000+ using an Arduino Uno:
Determining Controller Version
Unfortunately, there are multiple manufacturers that produce cosmetically similar STC-1000 controllers that are not based on the same chipset. As a result, some STC-1000's cannot be flashed with the STC-1000+ firmware; you have to have the correct version.
To determine the version of controller you have, open the controller as shown in the video above at about 2:47. Once you have the board visible, look at the location highlighted below; if the board says A400_P, Version: 1.0 you have the correct board and can flash. If it says something else (the most common "bad" board says S1000-Power_V1.1), there is not currently a way to flash it.