v0006 has been uploaded and should have connector placement compatible with the UBC "Tinah" shield (which is supposedly compatible with Wiring 0003.)  The same zip file has the v0005 with the slightly newer pinout.

Aside from the changed placement of connnectors, the older board does not have an Analog Reference input; only (apparently) power pins on that connector (which has only 4 pins in that rev.)   There is in fact not room for the new 6pin connector (it runs into the mounting hole), but I changed it to a 5pin connector with Aref "squeezed in."

The V0001 (?) picture that's floating around shows a 10pin JTAG connector in that location, BTW.  It's a shame that the history of the changes between the initial version and (say) the Sparkfun version have been lost.