Rx0 and Tx0 are going out to a separate FTDI header on the end of the board (like the Pro Mini), That way the FTDI UART and D0/D1 pins are separate signals. The JTAG pins go to a similar header, on the other end of the board. Those two headers will stick "up" from the board so as not to interfere with the two main rows of pins that are meant to insert into a breadboard or ZIF socket. If you look at my first post, you can see the two headers on the ends in the board pic. I've just shrunk it to be 2 pins shorter in length (removing Rx0/Tx0 from the main pin rows and connecting a secondary oscillator to TOSC1/2). RxLED/TxLED are currently not brought out to any external pins. I may end up connecting them to an external pad, since now that I've shrunk it to DIP-28, I could always backtrack to DIP-30 and add those extra 2 pins back (DIP-30 is a standard package, right?), then I'd have all of the I/O pins broken out except C6/7, which are connected to the 32kHz crystal.
Edit: Just realized you were asking about software mapping of pins. On the Goldilocks (which is what I'm basing my pinout off of), the I2C and JTAG pins don't seem to be assigned D#'s, they're just assigned signal names. I may be wrong, I'll have to look a bit more into the board definition files...