I'm not sure if you have checked the following, so here goes...
Regarding the AF-Assist Illuminator, there are some conditions where it does not operate. To quote from the D700 manual (p. 290):
The AF-assist illuminator lights when lighting is poor. AF assist illumination is only available when both of the following conditions are met: 1. Single-servo autofocus is selected for focus mode (pg. 72). 2. Auto-area AF is chosen for AF-area mode (pg. 74), or single-point or dynamic-area AF is chosen and the center focus point is selected.
Regarding the in-focus beep, there are also some conditions where it will not sound. From the manual (p. 298):
Choose High or Low to sound a beep when the self-timer is used or the camera focuses in single-servo autofocus (note that a beep will not sound if Release is selected for Custom Setting a2 (AF-S priority selection, pg. 284).