Might be a late post since you were scheduled for the Dec. 30th, but I've done that float many times in inflatable kayaks, never a pontoon.
At flows below 1500 cfs, you may scrape bottom in areas/half to get off and get to faster moving/deeper water.
The only real areas of concern are the first two rapid sets, especially the 2nd. But at anything below 2,000 cfs, you should be just fine. My friend and I rafted it at 5600 cfs last spring and got dumped into a hole at the second set of raps after launching at Big Eddy. We lost 1 paddle, sunglasses, and a few other items that we were wearing but saved everything important in the dry bag attached to the kayak.
He managed to avoid the hole and only got tossed around for about 5-10 seconds. I fell right into the hole and got worked for about 30 seconds where I was constantly tossed around like a dryer. On a side note, if you ever find yourself in that situation, get deep away from the power of the water on top and it'll spit you out. I made the mistake of stroking for the surface over and over and over to no avail until I got more horizontal and ball-like and stopped fighting it. It's the one time where I was extremely thankful for having a high degree of water confidence in order to remain calm.
But I've taken my wife and friends many times when it's 1500-2000 cfs without any issues. I wouldn't take out anyone that isn't confident in water and experienced when it's running 4,000+. I don't mean experienced by being a strong swimmer, I mean knowing how to navigate whitewater and avoid holes, strong eddys, rifts, etc. You have to have some skill with the paddle above 3,000 CFS. Typically you can steer clear of any forthcoming obstacles (fallen branches/trees, etc) as long as you pay decent attention.
Since you noted in your post, at 3,000 cfs in a pontoon you run the risk of being dumped more so than 2,000 or less. The river can act/look COMPLETELY different given just 1,000 +/- CFS change. All in all, the whole float down to the Sultan bridge has about 5-6 solid set of rapids you need to be locked in for.
Except a 3-4 hour float at 1,500-2,500 cfs.
Have fun and be safe!