I've had a stomach flu and now have bad indigestion which is uncomfortable, is there anything i can take or should i just let it run it's course?

If gastroenteritis: is ongoing then drink clear liquid like water, soda that is clear, or sports hydration drinks. Sip, sip, sip. Work up to solids w bland foods like bananas, rice, applesauce, toast, gelatin, or chicken. Avoid alcohol, nicotine, caffeine, dairy & high fat foods. Rest. If you are beyond the worst of it and have residual indigestion then you can drink slightly flattened ginger ale or nibble on >

Probiotics: Avoid all grains and lentils, milk products for a few weeks at least. Take a good probiotic like MegaFood MegaFlora Plus, daily. Consume plenty of fresh vegetables, flesh foods. Get some sunshine for at least 30 min/day around noon. Alternatively you can take vit D3 5000-10000 Iu/day for expedited recovery.