You might consider trying digestive enzymes. With a dietary change, the body takes time to adjust. Supplemental enzymes may help you through the adjustment period.
A second suggestion is to chew your food more thoroughly. Grandma used to say "chew your milk". The saliva starts digestion.
I love flax. Making a pudding seems like a tough way to take it. I prefer mine mixed with yogurt, sprinkled on salad, mixed into soup (it thickens the soup nicely), mixed with breakfast cereal, etc. Drink plenty of water with it.