The circadian rhythm could definitely be playing a bigger role than the vitamin D.

This is a great video about how light effects humans. https://www.youtube.com/watch?v=5YV_iKnzDRg

The part of that video that jumps out in my mind in regards to your problems is when he talks about digestion. If I remember correctly, he says that digestion slows to a crawl at night to try and let you get a solid night's sleep without waking up to go to the bathroom. When your eyes are exposed to the bright morning light, it triggers your digestion system to speed back up and finish processing the food you ate yesterday.

I imagine if you are working at night and only seeing artificial lights, it might not be bright enough to get your digestion moving at it's normal speed. Then since you're sleeping during the day, it's slowed down during the day too.

I could definitely imagine that causing some stomach issues.

If that is what is going on, then the cure for that would be looking at a very bright white light very close to your eyes. Vitamin D wouldn't help much at all.

Something like this might be helpful: https://www.amazon.com/Verilux-HappyLight-Lucent-Bright-Therapy/dp/B079YBGPM5/