InstancedBufferGeometry and Godrays not working properly

Questions
1

I am working on recreating an experiment similar to boiler, and I have come across a weird problem I cannot figure out. I can get the godrays to cast out, but somewhere in my occlusion pass it seems that each object is just a little bit off because there is issues with where the red objects are compared to the occlusion objects. My pictures show the example.

This is the result I get with my instanced objects:

I implemented volumetric god rays this way:

This is my rendering setup:

    requestAnimationFrame(this.animate.bind(this));

    if (this.params.animate) {
    this.simulation.shader.uniforms.time.value = performance.now();
    this.simulation.render();
    (this.mesh as any).material.uniforms.curPos.value = this.simulation.front.texture;
    (this.mesh as any).material.uniforms.prevPos.value = this.simulation.back.texture;
    (this.occlusionMesh as any).material.uniforms.curPos.value = this.simulation.front.texture;
    (this.occlusionMesh as any).material.uniforms.prevPos.value = this.simulation.back.texture;
    this.simulation.shader.uniforms.init.value = 0;
    }

    if (this.params.postprocessing) {
        // show the objects in the occlusion scene
        this.camera.layers.set(this.OCCLUSION_LAYER);
        // set a black background for the render
        this.renderer.setClearColor(0x000000);
        // render the occlusion scene and apply the volumetric light shader
        this.occlusionComposer.render();

        // show the objects in the lit scene
        this.camera.layers.set(this.DEFAULT_LAYER);
        // set a new background color
        //this.renderer.setClearColor(0x000000);
        // render the lit scene and blend the volumetric light effect
        this.composer.render();
    } else {
        this.renderer.autoClear = true;
        this.renderer.render(this.scene, this.camera);
    }

My occlusion mesh is just a copy of my regular mesh, but it is black for the occlusion pass. The simulation just ping-pongs back and fourth between my texture and changes the x,y,z and w for the objects position and life.

Occlusion mesh:

    this.occlusionMesh = new THREE.Mesh(this.geometry, new THREE.RawShaderMaterial({
        uniforms: {
            curPos: { type: 't', value: this.posTexture },
            prevPos: { type: 't', value: this.posTexture },
            resolution: { type: 'v2', value: this.resolution },
            color: { type: 'v3', value: new THREE.Color(0x000000) }
        },
        vertexShader: this.materialVertexShader,
        fragmentShader: this.materialFragmentShader,
        side: THREE.DoubleSide
    }));
    this.occlusionMesh.layers.set(this.OCCLUSION_LAYER);
    this.scene.add(this.occlusionMesh);

Regular Mesh:

   this.material = new THREE.RawShaderMaterial({
        uniforms: {
            curPos: { type: 't', value: this.posTexture },
            prevPos: { type: 't', value: this.posTexture },
            resolution: { type: 'v2', value: this.resolution },
            color: { type: 'v3', value: new THREE.Color(0xFF3344)}
        },
        vertexShader: this.materialVertexShader,
        fragmentShader: this.materialFragmentShader,
        side: THREE.DoubleSide
    });

    this.mesh = new THREE.Mesh(this.geometry, this.material);
    this.scene.add(this.mesh);

Geometry:

    this.bufferGeometry = new THREE.BoxBufferGeometry(3., 1., 2.);
    this.geometry.index = this.bufferGeometry.index;
    (this.geometry as any).attributes.position = (this.bufferGeometry as any).attributes.position;
    (this.geometry as any).attributes.uv = (this.bufferGeometry as any).attributes.uv;
    (this.geometry as any).attributes.normal = (this.bufferGeometry as any).attributes.normal;

    let lookup: number[] = [];

    for (let i = 0; i < this.size; i++) {
        for (let j = 0; j < this.size; j++) {
            lookup.push(j / this.size);
            lookup.push(i / this.size);
        }
    }

    this.geometry.addAttribute('lookup', new THREE.InstancedBufferAttribute(new Float32Array(lookup), 2));

Texture for x,y,z and w:

    // Each object has an x, y, z, and w
    let positions = new Float32Array(this.size * this.size * 4);

    for (let i = 0, l = this.size * this.size; i < l; i++) {

        let phi = Math.random() * 2 * Math.PI;
        let costheta = Math.random() * 2 - 1;
        let theta = Math.acos(costheta);
        let r = 100 - (Math.random() * 10);

        positions[i * 4] = r * Math.sin(theta) * Math.cos(phi);
        positions[i * 4 + 1] = r * Math.sin(theta) * Math.sin(phi);
        positions[i * 4 + 2] = r * Math.cos(theta);
        positions[i * 4 + 3] = Math.random() * 100; // frames life

    }

    this.posTexture = new THREE.DataTexture(positions, this.size, this.size, THREE.RGBAFormat, THREE.FloatType);
    this.posTexture.needsUpdate = true;

    this.simulationShader = new THREE.RawShaderMaterial({
        uniforms: {
            source: { type: 't', value: this.posTexture },
            seed: { type: 't', value: this.posTexture },
            resolution: { type: 'v2', value: new THREE.Vector2(this.size, this.size) },
            time: { type: 'f', value: 0 },
            persistence: { type: 'f', value: 1. },
            speed: { type: 'f', value: .05 },
            spread: { type: 'f', value: .2 },
            decay: { type: 'f', value: .5 },
            init: { type: 'f', value: .1 }
        },
        vertexShader: this.simVertexShader,
        fragmentShader: this.simFragmentShader
    });

Let me know if you have any ideas or if I need to include more information.