Hi dominicm, I am messing with programming Arduino over Bluetooth as well and looked at the same article. I believe one of your issues is potentially with the baud rate setting of the BT module. I believe if you are programming an Arduino Pro Mini (with the Atmega 328p chip) you need to set the rate at 57600. See here, for the results of my digging around on the subject: Arduino program / sketch upload speeds – 42 Bots
If you have the 3.3V, 8 MHz version of the Pro mini, you are correct to assume you do not need the two resistors for the voltage divider.
I believe the capacitor is there to adjust the timing of the reset. You might be able to use other values successfully as well, but better find some 1uf caps, if you want to be sure. I was able to manually trigger the reset - pushed the reset button as soon as the IDE message changed to "Uploading..." and the LED on my Bluetooth module indicated a connection was established. Of course that somewhat defeats the purpose of this, but it helps to test out the BT communication.
I am taking a different approach on the resetting though, once I verify it works I will post it as well. The idea is to use a 555 timer in mono-stable mode to do the reset.