Hi Poul,
I would guess the 100ns granularity should be already overkill, giving an error in the order of 1e-7. To be compared with mains instability of >1e-5:

http://www.leapsecond.com/pages/mains/

I would try to keep it as simple as possible... maybe even only one IC, there exist USB-capable PIC controllers (don't know about AVR, but likely as well).

Regards,
Achim

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