In 2003 I rode the Great Divide North to South on a Cannondale T800 touring bike. I had it set up with mountain bike bars and gearing, and 700cx45 T2000 Continental touring tires (AKA 29 inchers). The rigid fork worked fine, some of the washboard at certain speeds was annoying---but I don't think a suspension fork handles that stuff much, if any, better. I used thick grips on the bars and also on the bar-ends which helped avert numb hands. I used panniers which worked okay. I had a bolt break and another fall out on the front rack. The drawback to panniers is it takes longer to load them in the morning, and for the long dry stretches in Wyoming and New Mexico it is harder to attach an extra gallon of water to the panniers than a trailer. On the blacktop my bike was definitely faster than a mountain bike with trailer. I also had a suspension seat post, but I'm not convinced that did too much for me.
Hope you enjoy your trip! I sure enjoyed mine!