I have one of these boards for my arduino also and I'm in the process of trying to figure out how to connect it to the pi. On mine I seemed to be getting some kind of 'noise' if I tried connecting an FTDI 5v directly to the tx/rx holes on the arduino pin-out with the hardware tx/rx jumpers configured if I was using 115200 or any other high baud rates. I was able to get clean data at 19200 which is the speed they used in their 'passthrough' script and also tested that script through the arduino itself.
I noticed, however, that they have a 'uart' connector that appears to go directly to the 2v8 logic pins on the sim900 itself - or claims to. I wasn't able to get any kind of response out of it testing with a 3.3v ftdi. I noted they had a 'third' jumper configuration image on their wiki that was labelled 'uart' so I tried moving one jumper to the center two pins (rotated) and didn't have any luck there either. I sent an email to their tech support asking how to get the uart to work but I'll have to wait for a response. If anyone has ever used the uart on these things, I'd appreciate knowing anything you found out or did to make it work.
If I learn anything new, I'll try to find my way back here even though it's an old thread to post anything I find.