In assisting a patient on a CH forum, and in consultation with an experienced headache specialist, we did once pick up a misdiagnosis of CH, in a female, in her 30s, with MS.
The one commonality, was that frequency, severity and duration data for CH did not quite match, but it took a true CH'er to spot it, because it was very, very similar.
My headache specialist had seen only one other case of PH in a lengthy and international career. PH is rare, but affects more women than men, that was our first clue.
What this woman had, apart from terrible MS, was de-myelination of nerve sheaths and the resulting headache (Secondary Headache to MS in her case) was called Paroxysmal Hemicrania (PH).
I know you've had CH prior to MS... I also know personally how any headache "diagnosis" may have stuck for many, many years and that it may be right or wrong. It may be worth looking at your MS, other causes of "cluster-like" and secondary headache and doing this with a second set of eyes on it, a second opinion.
In the previous Woman's example, we got a second opinion and had a Neuro overturn her long time CH diagnosis, check her Indocid (Indomethacin) response and there it was, Paroxysmal Hemicrania. She responded to Indocid "absolutely" and immediately (CH'ers generally don't). She was she pain free within days on the correct medication, was free of the burden of CH misdiagnosis, and it cleared the way for some much needed PH and MS treatment. She has been doing better since and has been better equipped to raise a child whilst having MS.
She was also absolutely certain that her problem was CH, and it turned out that it was not. So, it may be worth a second opinion, even if you've done as we probably all have here at one time or another - laboured under one diagnosis for a long time. I was misdiagnosed for 25 years with Migraine, and for most of that time vehemently believed it to be true, with the same strength of assertion that you do.
She simply showed her Neurologist this piece:
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And the correct differential diagnosis was made.
Pain free in under a week, and all she did was to visit a forum, keep an open mind, and ask her Neuro for a review.
He checked Indocid response, as he should have and she was pain free.
If you're looking down the barrel of CH and MS, (or even PH) I would still recommend getting an alternative pair of eyes over the D3 regimen. Your Dr. clearly needs to go back to medical school and read up on D3 toxicity, in which he will invariably only be trained in treating deficiency, not treating disease - a very different ball game. There is much ground to be gained with the D3 regimen, outside of CH too. Any specialist worth their salt will treat the regimen seriously, as many now are doing.
Neurology Journal thought it was safe enough and had enough merit to publish it: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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Maybe show your Dr. that paper. If you get more claims of "toxicity", maybe it's time for a new Dr. and/or specialist.
2nd opinions have got many of us out from under the burden of CH before.
I think Batch's opinion on using D3 in CH was about opinion #963 for me, but that's the second opinion that worked, now endorsed by my headache specialist and Neuro. (Don't count me again Batch, I've completed the survey and you have my results).
Never stop looking for answers, that is key!
Hope this helps.