Yep need pre conditioner, Charles Neils, best stuff you'll ever buy..here is video too. Is that Poplar your trying to stain. I did a poplar piece not long ago, used Neils pre-stain came out great, which is hard to do with poplar.
It's red oak. The top is maple and sweet gum with paudak miter keys. This whole thing has been a disastrous learning experience. My shop isn't heated or insulated so my wood keeps moving and stain looks weird. Should have stained before the keys I've learned too! This thing is shot, notice I had to plane one side a lot thinner. Cant remember why but it caused the side to split open.
From what I can see it looks like most of the problem is insufficient sanding. Red oak normally doesn't need a wood conditioner. It's woods like maple, pine and alder that are prone to blotch. When you build a box it's a good idea to sand the inside side of the parts prior to assembly. That way you can thoroughly sand it with an electric sander. It should be the only sanding after assembly is if you get glue on the wood and wipe the wood down with a wet cloth. The second picture in post 1 does show a glue stain. If you wash the glue off with a wet rag all you would need to do is a little fine sanding by hand to smooth the wood out where the water raised the grain. It wouldn't leave a spot where the stain wouldn't take. In post 4 the picture at top right shows a lateral line on the center piece of wood. This looks like the mark made by the planer when the board was surfaced. I would sand this line out. The picture at top left looks like you made the bottom too big and the joint didn't pull together at the corner.
You can save it by making it look old and distressed IF you choose. I probably would save the top for another project or a remake of this same size box.
The red Oak can be dented and scuffed up and then sanded with a disc to create saw swirls. Then take some black spray paint and rub it into the newly created dents and scratches and wipe it out before it dries. You make have to reglue the split with some 2 part epoxy to get it to hold. Bring the dang thin into the house so it will stabilze in a constant temperature..... White paint will work also for a more antiques look. If you can find some crate wood or barn wood that would make a good top.
It not about perfection. It's about learning and making your "mistakes" look intended. Here's some examples of distressed boxes:
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