@nikkyuze,
I thought your questions about indomethacin would benefit from the input of a Mayo Clinic pharmacist. This is information she offers:

"Gastrointestinal side effects of NSAIDs like indomethacin tend to be dose related. Have you been tried on a lower dose of Indocin? I am wondering if a lower dose and/or using the immediate release instead of the sustained release formulation might provide relief with less side effects. Your doctor could have you taper slowly down to the lowest dose that provides relief. Doses of indomethacin immediate release 25 mg taking with each meal have been shown effective. Indomethacin suppositories could be tried although there is conflicting data regarding whether these would have less GI adverse effects. Celebrex may be another option. It would be easier on your “guts” but may not be quite as effective as the indomethacin. I hope you can get some relief. I can imagine how frustrating it would be to have to balance the symptoms of hemicranias continua with the side effects of treatment. Be sure to communicate with your care provider regarding the gut pain you are experiencing."

@nikkyuze, have you talked to your doctor about trying a different dosage?