Check and make sure your texture path is indeed:
src/main/resources/assets/<modid>/textures/block
and not
src/main/resources/assets/<modid>/textures/blocks
It's a common mistake.
You can view what minecraft does but, I'm not familiar with IntelliJ and were to look for it though. There should be a Reference Library you can peruse through for the source code of minecraft.
In your development environment, /data/minecraft/tags/blocks add your walls AND what minecraft has in their JSON. I had a similar problem and, this fixed it.
No, it just tells the leaves how far above ground level to generate.
I did figure this out. Overriding the leaves, and logs, tag in resources/data/minecraft/tags/blocks solves this issue.
Do the same for your logs.
I have based my custom tree off of the spruce tree but, when I bonemeal it to make it grow, the trunk is only 1 block high (with random 1 more) and, the leaves generate as they should. Just no trunk to the top of the tree.
Tree Class
Sapling Class