ok you dont need the jtag connected once you have updated the bitstreem.
and it's how the clip attaches to the NAND chips that is the issue here
do you have a good closeup pic of it attached to each NAND?
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from the link you posted:-
in the description:-
1- Redesign of main board now more small and stable (4 layers)
2-
Slave baord with USB, LED, SWITCH (for memory banks selection)
3-
FCC cable 15 pins that allow to connect externally the slave board
the Slave Board is the JTag
its the 2 items in the pic (progskeet 1.2 + Slave Board)
and you say you are getting the NAND connector aswell?
so thats 3 items
and 3 items is what you need (assuming the NAND connector fits both ps3 boards)