Wood – What material is used to fill cracks in wood that looks black afterward

Good for you for tackling this project. If you're an amateur and this is your first project, then don't try to be perfect because you will be beating yourself up for no reason.

If you are going to paint the finished project, then the looks don't matter so much. You can buy wood filler that will fill any gaps and grain. Force it into any gaps or cracks with a putty knife, and then sand smooth afterwards. If needed, start with a coarse grain sandpaper (otherwise start with medium) and then progress to fine. Wood filler can create fine dust, so use a dust mask while sanding. For panels, I would recommend using MDF as it has a very smooth surface for painting. Cutting MDF creates a LOT of dust, so always use a mask and remember that it's better to do this outside or with a dust collection system.

This is an interesting question. I just read the wikipedia article on orange oil. While this stuff comes out of an orange and is widely thought of as "natural" and "organic" and "safe", it seems like a pretty good description of it might be "turpentine from an orange".

I don't think you are likely to get an accurate and definitive answer to your question. No matter which way you go, you will be taking a small risk.

If you think about it...all wood came from a tree, and most trees have some bugs in them. One would think that kiln drying would kill the varmints, but who knows for sure?

If it were me, I would just finish it in the normal way and keep an eye on it after bringing it in the house. Your mileage may vary.