Hey MJ,
Great News! The general, mild headaches (global/bilateral) should clear in a few days... Make sure your wife has started the 3-month course of vitamin B 50.
Regarding the number of pills taken in this regimen... I've shopped around and there are a few things you can do to lower the pill count.
1. Buy the 10,000 IU vitamin D3 gel caps - your wife will only need one a day as a maintenance dose. Puritan's Pride has a great offer on 500 capsules of 10,000 IU vitamin D3 (5 bottles for $33.95) or 6.7 cents per 10,000 IU capsule.
Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

or

2. The Kirkland brand Mature Multi contains most of the vitamin D3 cofactors plus 220 mg of calcium. Only one capsule a day is needed. When the three month course of vitamin B 50 is complete, the Mature Multi contains enough of all of the B vitamins to prevent any further insufficiencies.
3. I take two of the Nature Made Omega-3 Fish Oil liquid soft gels and one of the Nature Made 400 mg magnesium liquid soft gels...
4. Adding the Super K with advanced K2 complex will bring the pill count to 6... 7 while taking the vitamin B 50.
Henry Lahore, the vitamin D3 Jedi Master at VitaminDWiki has gathered some excellent data on vitamin D3 and all the cofactors.
The following link is loaded with great information on vitamin D3 so should be required reading for all CH'ers.
Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

or

Henry has web crawlers running 7X24 picking up everything related to vitamin D3 including the latest RCTs. He posts the links or quotes these web articles as is, so it's best to be a critical reader.
You'll find good, bad, and other articles... Some very compelling and supportive of vitamin D3 therapy while some are obviously biased against its use...
If you dig deep enough on the bad articles... you'll find Big Pharma or their disciples involved in studies trying to scare people away from taking vitamin D3...
Henry is also good at pointing out poorly designed studies... or studies with conclusions that are not supported by the study data or design.
Henry also points out that most RCTs involving vitamin D3 are conducted at too low a dose (≤2000 IU/day) to obtain significant results and nearly all are conducted without any the vitamin D3 cofactors...
The two supplements in the anti-inflammatory regimen that cause the most GI tract problems are the Omega-3 Fish Oil and magnesium. Both, along with vitamin D3 and the rest of this regimen are best taken with the largest meal of the day.
It doesn't matter if you take these supplements and then eat, or eat first and then take them... As long as they're in the tummy with lots of food... you'll get the best absorption and least amount of GI tract problems.
I've found the 400 mg Nature Made magnesium oxide liquid soft gels to be as effective as the magnesium citrate and both are about equal in their capacity to trigger osmotic diarrhea... Henry likes the magnesium chloride...
The magnesium is clearly the culprit responsible for lower GI tract problems so by all means, drop the magnesium dose from 500 mg/day to 250 mg/day for a week or two. That should firm things up a bit...
That said, due to the important function of magnesium in supporting the enzymatic processes that metabolize vitamin D3, I wouldn't drop the magnesium dose any further. I'd also try to raise the dose back up to at least 400 mg/day.
Good on you for starting the anti-inflammatory regimen along with your wife. Your brain, heart, prostate, immune system along with the rest of your body will love you for taking it.
If you haven't figured it out by now... I'm of the opinion the entire family should be on this regimen even if they don't suffer from CH... The health benefits are too good to ignore...
On top of that, with our healthcare system going down the dumper... staying healthy is the only logical alternative... and it only costs around 40 cents a day...
I have my entire family taking this regimen... my wife, brother, three kids, their spouses and seven grand kids.
My daughter has been on this regimen for nearly two years... She went through a problem free pregnancy and delivered a very healthy baby girl...
Her OB was a little hesitant at first about my daughter taking 10,000 IU/day vitamin D3 and all the cofactors during her pregnancy, but he's since determined 10,000 IU/day vitamin D3 is a great maintenance dose when taken during pregnancy along with the vitamin D3 cofactors, and... while breast feeding.
He now tests for 25(OH)D and makes sure all his pregnant ladies and breast feeding mothers have serum concentrations of at least 60 ng/mL.
Take care and please keep us posted.
V/R, Batch