I've read that exercise, cardio in particular tend to give persons indigestion. Maybe you need a Pepcid or Prilosec first thing in the morning.
But still, it seems your carb consumption might be too high. At least for me. I consume about a 24 fl oz. bottle with 150 Calories in it every 50 minutes of riding. That's about 180 Calories per hour. If I am planning on going all out on a max effort for several hours then I might put 200 to 250 Calories in each bottle.
Your stomach can only absorb so much. So if you are over supplying it with carbs, proteins and fats, then it's going to let you know by making you feel lousy and perform lousy.