Jr-programmer and Nand-X both read/ write to the Xbox 360 nand over SPI so the signals used are the same. Its always best to know which signal/wire is going to which point on the mobo regardless of wire colour just in case u lose the original wiring. ie.
MOSI - J1D2.1
SS - J1D2.2
SCK - J1D2.3
MISO - J1D2.4
GND - J1D2.6
EJ - J2B1.5
XX - j2B1.6