Just got off the run with my kayak on Sunday. If you're a solid class III boater you'll be fine above the confluence. After the Yampa comes in, you'll find big waves, big crashing laterals, boils, and whirlpools. Sometimes the boils and whirlpools show up in the middle of wave trains. I had to paddle upstream a fair bit to keep from out running the rafts in Split Mountain. You'll also find logs everywhere, some will be significantly larger than you in your kayak. The last day through Split I had the largest shit-eating grin I can remember having in my kayak.
"A witty saying proves nothing."
- Voltaire (1694-1778)