Are you sure the ACV isn't irritating your bladder? I've had lots of issues with painful bladder/non-infective cystitis alongside GERD for the last 3 years. The bladder problem started first - the stomach issues started after I gave up tea and coffee for my bladder issues (go figure)! The only sensible conclusion I've ever drawn is that my stomach issues make it difficult for me to drink enough fluid to keep my bladder happy.
I did find marshmallow capsules helpful for the bladder.
I've been having acupuncture for quite a while now too. In Chinese medicine terms there is a link between the stomach and the bladder to do with fluids and energy flow, but I don't know enough to explain properly!
All I can say is I've had both problems off and on for the last 3 years and have yet to find a common cause!
GERD (3 years and counting)
Lifelong stuff: Food allergies/intolerance, eczema, asthma