This is what I have for two ModelFiles, the first only applying one overlay and the second apply the first overlay + another.

public ModelFile scuffedWarenaiBlockModel(Block block) {
        return models().getBuilder("scuffed_" + name(block))
                .parent(existingMcModel("block"))
                .texture("particle", warenaiBlockTexture(block))
                .texture("underlay", warenaiBlockTexture(block))
                .texture("overlay", scuffedTexture())
                .element().from(0, 0, 0).to(16, 16, 16).allFaces((direction, faceBuilder) -> faceBuilder.uvs(0, 0, 16, 16).texture("#underlay").cullface(direction)).end()
                .element().from(0, 0, 0).to(16, 16, 16).allFaces((direction, faceBuilder) -> faceBuilder.uvs(0, 0, 16, 16).texture("#overlay").cullface(direction)).end();
    }

    public ModelFile crackedWarenaiBlockModel(Block block, int crackedLevel) {
        return models().getBuilder("cracked" + crackedLevel + "_" + name(block))
                .parent(existingMcModel("block"))
                .texture("particle", warenaiBlockTexture(block))
                .texture("underlay", warenaiBlockTexture(block))
                .texture("overlay1", scuffedTexture())
                .texture("overlay2", crackedTexture(crackedLevel))
                .element().from(0, 0, 0).to(16, 16, 16).allFaces((direction, faceBuilder) -> faceBuilder.uvs(0, 0, 16, 16).texture("#underlay").cullface(direction)).end()
                .element().from(0, 0, 0).to(16, 16, 16).allFaces((direction, faceBuilder) -> faceBuilder.uvs(0, 0, 16, 16).texture("#overlay1").cullface(direction)).end()
                .element().from(0, 0, 0).to(16, 16, 16).allFaces((direction, faceBuilder) -> faceBuilder.uvs(0, 0, 16, 16).texture("#overlay2").cullface(direction)).end();
    }

 

This works, but it doesn't seem so simple for a stair block. 

I copied the stair stuff from the forge BlockStateProvider class to get started with a normal stair model that works: 

public void warenaiStairBlock(StairsBlock block, ResourceLocation texture) {
        warenaiStairBlockInternal1(block, texture, texture, texture);
    }

    public void warenaiStairBlockInternal1(StairsBlock block, ResourceLocation side, ResourceLocation bottom, ResourceLocation top) {
        warenaiStairBlockInternal2(block, block.getRegistryName().toString(), side, bottom, top);
    }

    public void warenaiStairBlockInternal2(StairsBlock block, String baseName, ResourceLocation side, ResourceLocation bottom, ResourceLocation top) {
        ModelFile normal_stairs = models().stairs(baseName, side, bottom, top);
        ModelFile normal_stairsInner = models().stairsInner(baseName + "_inner", side, bottom, top);
        ModelFile normal_stairsOuter = models().stairsOuter(baseName + "_outer", side, bottom, top);

        warenaiStairsBlock(block, normal_stairs, normal_stairsInner, normal_stairsOuter);
    }

    public void warenaiStairsBlock(StairsBlock block, ModelFile stairs, ModelFile stairsInner, ModelFile stairsOuter) {
        getVariantBuilder(block)
                .forAllStatesExcept(state -> {
                    Direction facing = state.getValue(StairsBlock.FACING);
                    Half half = state.getValue(StairsBlock.HALF);
                    StairsShape shape = state.getValue(StairsBlock.SHAPE);
                    int yRot = (int) facing.getClockWise().toYRot(); // Stairs model is rotated 90 degrees clockwise for some reason
                    yRot %= 360;
                    boolean uvlock = yRot != 0 || half == Half.TOP; // Don't set uvlock for states that have no rotation

                    ModelFile shapeDependentModel = shape == StairsShape.STRAIGHT ? stairs : shape == StairsShape.INNER_LEFT || shape == StairsShape.INNER_RIGHT ? stairsInner : stairsOuter;

                    if (shape == StairsShape.INNER_LEFT || shape == StairsShape.OUTER_LEFT) {
                        yRot += 270; // Left facing stairs are rotated 90 degrees clockwise
                    }
                    if (shape != StairsShape.STRAIGHT && half == Half.TOP) {
                        yRot += 90; // Top stairs are rotated 90 degrees clockwise
                    }

                    return ConfiguredModel.builder()
                            .modelFile(shapeDependentModel)
                            .rotationX(half == Half.BOTTOM ? 0 : 180)
                            .rotationY(yRot)
                            .uvLock(uvlock)
                            .build();
                }, StairsBlock.WATERLOGGED);
    }

 

Now I have no idea where to go. I could take the time and figure it out all on my own, but since I really should be working on a college essay I thought I would see if anyone else knew what to do first. If not, then I will just do it myself when I get the time.

Update... I still can't figure it out. So, since the blockmodels are super custom while the blockstates and item models are your average ones, I have come up with the idea of only doing datagen for those two and just referencing the pre-made blockmodels which I will put into a subfolder of the models/block directory.

It will still be a little bit of pain, but at least my resources folder will stay organized which was my original goal.