The round legs are 0.46mm/0.018in diameter per their datasheet.
What do you mean by jumper pin diameter? That just refers to too many things.
The BobuinoII has an SD card, as does the Standalone programmer.
SD copier, not sure a 16 MHz processor is the way to go. SPI at 8 MHz clock only transfers 1 byte/uS max, a large amount of data would take a long time. Read 512 bytes in, send 512 bytes out, that's 1024uS, 1 mS, right there for a 1/2K file.
You can do the math for bigger files, like a 8MB MP3 file. 16 seconds at least? Be faster to put one card in a PC, copy it, put the second card in, copy it back out.