Glad to hear you got it working!
The issue with set up in the Make article is that the BT module can only be used to program the Arduino. As soon as it pairs with the PC, the reset will be triggered by the Bluetooth module LED pin.
I am triggering the reset from software, no hacking the BT module. Essentially, in software I keep track of the "mode": programming, or communications (default). If in programming mode, once I detect incoming serial data, I trigger the reset by pulling a digital pin low. Here is where the 555 timer comes in. Apparently, resetting the Arduino using one of its own pins is not a good idea (specified by the Atmel support and discussed elsewhere on this forum). So I have an Arduino digital pin trigger a 555 timer in monostable mode (one shot mode). Simpler set-up using just a 1uf cap between the digital pin and the reset pin also works, but I wanted to try the 555 timer IC anyway.
If in communications mode, I just use the Bluetooth module as usual. Sending a specific command (like "P" in my case) switches to programming mode. Hope that helps.