Honestly I don't understand why are you are going on such a complicated stack. Seems like overkill, increasing risk of iatrogenesis.
You need vitamin D and vitamin A. Those are the two vitamins depleted from excess K2. You could hypothetically add magnesium to that, just because it opposes calcium/coagulation - but that is just a patch. But hypercoagulation is not the primary problem with excess K2, it's secondary problem. Primary problem is activation of Matrix GLA protein and decalcifcation of saliva and costo-sternal cartilage.
The reason chemical vitamin D doesn't agree with you is because vitamin D inhibits NO. NO inhibits coagulation. When you get sun, you create tons of NO from the UVA, which supplements the body with NO in the face of Vitamin D, so you don't get platelet activation/thrombosis. If you take chemical vitamin D, you need to boost NO with things like beet juice and pomegranate, and reducing oxidative stress so NO doesn't quickly oxidize (which beet and pomegranate juice are both great at, coincidentally). Otherwise, take in non-narrow band UV (UVA and UVB), because UVB is needed for vitamin D, and UVA is needed for NO synthesis (although UVB does some NO synthesis, it isn't as much). You can also just take in more dietary nitrates, or use nitrate supplements. Exercise is another way to upregulate NO, via activation of eNOS. So if you do take chemical vitamin D and A, you can mitigate the side-effects by taking it before exercise with beet + pomegranate juice.
Vitamin B2 can play into this as well, by helping recycle Vitamin D. But again, vitamin D without NO is no good. Vitamin B2 is also cytotoxic to bacteria, so it lowers the production of NO from iNOS. I've experimented with B2 and have found it doesn't really help all that much, and in some cases makes things worse.
So think of Vitamin D, vitamin A, NO, magnesium - find the best ways that work with your lifestyle to get those and then keep them up in decent doses (in this order of dose/importance: NO -> D -> Mg -> A). That will allow you to tolerate calcium again. Sun is obviously the best way, but not accessible for us northerners year round.