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On the duo website they say to remove 2 pins from the connecter..
refers to pin 3, 4 & 5 from the female pin header which is soldered to the DuoX 2 chip.
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My board only has pins 4 and 16 missing.
refers to the male pin header which is soldered to the LPC holes on the xbox motherboard. If you use the 12-pin male pin header that comes with DuoX 2, you only have to remove pin 4 from the male pin header. However, your "professional" chose to use 16-pin male pin header (to screw you further by recommending X3 later after intentionally screwing up the DuoX 2 instal ?!?! ), so he removed the unused pin 16 which is OK.
As I said before, don't bother about the pin headers, just concentrate on redoing the LPC rebuild. Though wired LPC rebuild is more reliable / consistent, you can still repair the soldering for the LPC Rebuild PCB.
As others have mentioned, mod chip install, especially DuoX 2, on v1.6 is not difficult at all - any decent modder can make it work 100% without much difficulty. What a lame "professional" that doesn't even check his work. To me he is more like a con man than a modder!