Actually, I think I know what you are referring to with the micro-pause, as I too suffered from it. I cannot tell you why it happens, but I did manage to get rid of it by disabling VSync.
Now as a Movie-maker I like my VSync as it stops tearing of the cockpit frame with head movement, but the micro-pause (almost as you put it in a rythm) was a real pain!
Disabling VSync fixed the problem and I too run a pair of 8800GTS (G92) in SLi, so it could be a common problem.
Maybe it could work for you, but that's what fixed it for me.
Also for odd water problem, have you downloaded the very latest .dll's from the 1C forum, which fixed a host of problems for the 8800's?
Link is in fourth post from the bottom of this page:
http://forum.1cpublishing.eu/showthr...t=patch&page=4
Hope that helps, cheers, MP.