I agree with Ed's assessment of waiting for the peak of a wave, but must share one experience that has caused me to change strategy slightly. I am hesitant to offer this b/c I am not a "seasoned veteran" by any means, but I think this experience is worth sharing.
Earlier this year, I ran Shoshone at about 2500 cfs. On Superstition (the last big wave train rapid after Tombstone), the first wave was over 10' and flipped me b/c I was just plain being lazy, before I reached the peak. I set up in a tuck position, and waited for the first pause at the peak of the next wave to get my timing, and then prepared to hit my roll on the next pause, which I was fully anticipating (all in line with Ed's description). However, as I accelerated down the trough, I smashed my head with such force on a rock that I am very suprised I was not knocked out - I mean HARD. I still hit my roll, but was very disorientated (had to roll again on the minor run out waves), and was seriously trying to remember the day of the week when I caught the first eddy.
In my case, all of the impact was absorbed squarely on the top of my helmet, however this did transfer into my neck, leaving my neck and upper shoulder sore for about a week. Had the impact occured off to the side, or to the front on my forehead, I am sure there would have been severe damage to my helmet rendering me unconcious.
My main point is that even in the better scenario of deep water in big wave trains, there is still lots of danger. I know this rapid well - I thought I was in the middle, in very deep water, and I still found a rock. I suspect the waves were so big and the troughs so deep (and therefore creating shallower water), that the rock I hit was usually covered at the "normal" flows I run Shoshone at around 12-1800. In addition, the water was moving so much faster due to high flows, and my acceleration down the back side into the trough was so great, that the impact was very, very hard.
The only thing I offer is how this changed my strategy. If I am fully set up, and ready to go at that first pause, I am going for it. Had I hit my roll on the first pause (which I was basically ready to do), I would not have a story to tell. I am not staying soft side down any longer than I have to anymore. The most important strategy is to wait for the pause at the top of the wave, but I maintain to attempt a roll ASAP at the first pause if you are ready.
Just my 2c for what its worth.