The answer I got from IFI regarding the timing of the signal is:
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The channel data is adjusted to get values from 0 – 255 and the channel data spacing is 2ms.
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Meaning the signal that is sent out is basically the analog output from the different pots and switches in the controller using an 8-1 analog mux to select one channel at a time. Each output is transmitted for 2ms, and then they switch the mux to the next channel. I'm assuming that they go in order when switching channels, but I haven't looked into it. I'll scope the mux control lines just to make sure of the order.
This probably isn't going to be that hard to do. I'm going to use a PIC instead of the Basic Stamp (too slow). I'll look into this some more during the weekend, as I've got a lot going at work right now.