Yes, I use type 3 solder paste and an electric skillet to perform reflow. I then use a soldering iron and solder wick to remove any excess solder that might bridge two adjacent pins. Seems to work quite well.
I am wondering if perhaps there was a problem with the board from OSH park. If you look at the photo you will notice a flaw with the silkscreen printing at PD0:7. I am wondering if perhaps there was a flaw with the copper... If I connect the FTDI header to a computer, the LED D2 doesn't light, but that should be the case since you have that wired to pin and not as a power indicator? I can't think of anything else at the moment. I don't have your address readily available, so if you could IM it to me I would appreciate it if you would like to look at the board, if not I can put it on the shelf until I get time to work on debugging it.