Hi,
Be sure the dimension of the S5000X S5000XVNSAS fit with the xw6600 case, because they're not the same dimension, AND check the PSU connections to be sure it's the same as your original mainboard.
The original mainboard model of the xw6600 is 440307-001
http://www.serverworlds.com/hp-440307-001-xw6600-system-board-439240-001/
Regards,