Just as PPI's aren't always effective for everyone who takes them, herbs can also affect different people in different ways. So having said that, and hoping that you'll check out any advice you get with your healthcare provider, below are a few herbs that herbalists sometimes prescribe to treat disorders related to gastric acid production.
Licorice (Glycyrrhiza glabra) is often used to treat and prevent stomach ulcers. You’d want to take the deglycyrrhizinated (DGL) form because the pure form can cause problems with blood pressure. The DGL form comes in wafers and tablets and has very few side effects.
Aloe vera gel extract is believed to decrease the production of stomach acid, however sometimes you need to take it for several weeks before it starts to work. It is also an anti-inflammatory agent which can be beneficial. You would want to make sure that the extract was commercially prepared and didn’t contain any aloin or aloe-emodin. Don’t use aloe juice either because it can cause diarrhea.
The Ayurvedic and Chinese traditions use Turmeric (Curcuma longa) to treat digestive disorders. You have to be careful though because too much turmeric can have the opposite effect and actually cause ulcers. This is where it's important to be treated by someone who knows what they're doing.
Since you mentioned altered stools, you might want to look into Bilberry (Vaccinium myrtillus). It is used widely in Europe to treat bowel problems. It comes as an extract or as dried whole berries (which, when crushed, are used to make a tea). Avoid fresh bilberries though because they can cause diarrhea.
Sometimes Peppermint is used to treat bowel problems but it is not recommended for people with acid reflux since it can be irritating and aggravate existing problems.
Curious George mentioned this already and even though it's not an herbal treatment, acupuncture and acupressure (often in conjunction with herbal treatments) have been used to effectively treat severe acid reflux. So you might want to consider that as an option as well.
One other word of caution, if you’re taking PPI’s because it’s been determined that you have an H. pylori infection, herbal treatments aren’t usually a good substitute, though they can be a great complement.
I hope you find a solution that works for you!