OK well just took a wild stab and it seems to be 100 times better, although not completely taken care of. Since earlier some signs were telling me that the crank trigger was the likely cause of this, I decided to enable crank only filtering. I used the Tach Rejection feature, and set it to 30% as that was a value I had seen thrown around in the filtering documentation on here. And what do ya know, the issue seems to have 99% gone away. You'll see in this video that it still lost sync a couple times under WOT, but way better than before. I will play with filtering a little bit more and hopefully be done with this issue.
One thing I did notice was that in the composite log, the crank now shows up as a square wave instead of just a single edge as it did before. No idea what that means however.
http://www.youtube.com/watch?v=EZPwl3fj34I