I used to take D3 in the morning with breakfast, but now I take it at bedtime with magnesium - they work together to aid sleep.

I think you should be fine talking them with your biggest meal, but if it were me would try to break the supplementation across your meals - 1,2,3 or more a day. This is what I do, and it works out really well.

If you were taking alpha lipoic acid or acetyl l carnitine, I might suggest taking it with your coffee in the morning, as it is a nice pick me up. The supplements you listed seem to be best taken with a meal.

My understanding is that among the various types of supplements vitamins tend to be energizing. If your BP coffee has a reasonable amount of healthy fat (butter and/or coconut oil?), then you might try taking your vitamins (D3, K2, C) with it in the morning.

Supplementation, unless in the case that you need it to aid some sort of activity (pre workout?) or recover (post workout?) is not something that is timing dependent. Especially in the case of stuff like Omega-3s, and minerals, just hitting the goals, regardless of when they are hit is sufficient.

That being said, some things might and should be taken away from bedtime, and others closer to, depending on the stimulative or depressive nature of their use.

I've read to only take D during the day or morning because of the sun emulating effects. Cod liver would be the same because of the D content. I personally take mine in the morning with my Bulletproof coffee.