Sleep disturbance is a time-local short-term effect, it isn't obvious to me that it indicates problems with long-term consequences.

Why do you think humans sleep at all if sleep disturbance has no long term effects? I think it's fairly straightforward to think that humans do undergo processes that further health during restful sleep. After quick Googling http://www.ncbi.nlm.nih.gov/books/NBK19961/ is a study that says so.

Your links say that the timing of vitamin D intake affects sleep. Fine, but that's not really what most people take vitamin D for. There is a variety of claims for vitamin D supplements which generally have to do with bone health, viral infections, CVD, etc.

Bone health might be just about Vitamin D's role in calcium absorption.

From the paper I linked above:

Sleep Loss Is Associated with Cardiovascular Morbidity

Sleep loss and sleep complaints are associated with heart attacks (myocardial infarction) and perhaps stroke, according to several large epidemiological studies

I can't find talk about viral infections on that page but I would assume that you can also make a case that a sleep deprived individual is at higher risk for them.

Why? "Stupid" is a strong word.

Investing tens of millions in experiments based on a hypothesis that you don't really test is stupid. To use the words of Feynman you could also say cargo cult science with Feynman used to describe the rat psychology experiments of his time.

If your hypothesis is that timing matters but the blood level doesn't matter, what's the underlying biochemical mechanism?

When I say blood level I mean the level you measure when you give a individual a blood test every month and make a study based on that data. I don't mean the level you would get if you measure every minute.

But I don't need to point to a biochemical mechanism to validate an empirical observation. Currently drugs get often designed based on an idea that you want to target a biochemical mechanism but when they do work, the work in mysterious ways that aren't exactly the way the people who designed the drug would have thought beforehand. Of course most of those drugs fail anyway. It's much better to focus on things that produce empiric effects than going to deeply into theory.

But as far as vitamin D goes, there plenty of evidence that it can work as a hormone. It also a hormone that gets naturally produced at specific times as the sun usually shines at specific times of the day and not at night.

How would you know how much of vitamin D do you need?

The empirical method. You can take different amount of vitamin D and see the effect on yourself. That means you have either good awareness of your own body, QS tools or both.

Coming to your own judgments instead of trying to follow what some authoritative doctor or doctrine tells you is what Kant described in his day's as his ideal of enlightenment. The way is real empiricism. Paying attention to real world feedback.