Elderberry is a very acidic fruit and a lot of people find that too much acid gives them stomach ache. Depending on how long you did this for, you have probably altered the acid levels in your stomach and made it more acid. If you have too much acid, then you are likely to have stomach ache. What you need to do is try to restore this balance, by eating non acidic forming foods. This means cutting out fruit for a while. You could also try drinking a little milk if you don't have problems with it. This coats your stomach and can settle it and help stomach ache.