Thanks for the kind words.
We still haven;t got to trying it out at our end, however I understood what you want to do. SPI is usually way more reliable and hence we usually recommend it.
You can use the FTDI code to remotely upload the code too, however in that case it would be connected to the USB port on the Pi instead of your computer. Not an ideal way to do it but it would work.
The other was is to use the Arduino Bootloader and use the Serial pins on the Arduberry. There are a lot of different settings to try out to get this way to works, if it works at all. We will try it out this week and let you know if it would work or not.
Also, can you tell me a little more about the project you are building. I might be able to help you find alternative ways that might be better/easier.