Ok, did a little more experimentation over lunch.
I tried several of the driver sets out there and they didn't really make a gigantic difference but I did find something that did!
I had been using the individual driver profile settings to set either SFR or single GPU.
This time I went to the harder driver switch of Single GPU or on the 174 drivers dual display mode. This effectively really does turn SLI off. Currently I am testing this with the 174.xx driver set. (174.74 I believe) ( the 174s I hear were the last to really take the 9800gx2 in to account)
Well, this did make a difference, even with Vsync on (since I use Track IR) the stuttering went way down and I think may be even gone. I don't want to get too excited because I didn't have a lot of time to test it. But after work I'll give it a real run through. So I believe this leaves me with 1 8800GTS for IL2 which seems to keep a good 60fps so far.
Now the stutters I've had in the past have probably been for a variety if reasons and that is the hard part. It might not have always been the same cause but always the same symptoms, very frustrating.
I was considering getting a new card soon, either the 285 or 295. I think this whole thing has soured me on the SLI on 1 card variety. Perhaps the 285 is in my future.