Giving your digestive system a break by fasting is the most efficient way to improve it's function. Alkaplex Green+ is a good supplement to add for this purpose. Loads of vegetables should be consume too, no matter what IMO.
Take 1 tablespoon of Braggs apple cider vinegar after each meal to help break it down. If you don't have apple cider vinegar get some Hydrochloric acid. Also, the enzymes will help break down the meal and get all of the nutrients to the right place.
If your stomach is really messed up, you might want to get a good probiotic and do a therapeutic does for a week and then go down to a maintenance dose after that.
Citrus fruits such as orange, grapefruit, lemon, guava, grapes etc. and citrus fruits juices are more beneficial for the digestive system.
I take these citrus fruits and vegetables salad to improve my digestive system.
I take Dr. Stephen Langers Ultimate 15 strain probiotic as I got a great BOGO deal on Swanson's site...also take BioCor digestive enzymes before meals and both MultiLife multivitamins and my greens powder have digestive enzymes...
You're taking too much calories per day and to improve your digestive system you should start eating fresh fruits,veggies salad because it proves to be very helpful in improving digestive system and also you can eat less then before.