Raytracer mesh not centering correctly

Question

I have had this bug for a while, and I tracked it down to the way I am trying to rotate and then center a mesh in my raytracer. The way I figured it out is the meshes need to be rotated first, and then centered with the bottom center point of the mesh at 0, 0, 0. Here is my code:

    for(int i = 0; i < triangleList.size(); i++) {
        for(int a = 0; a < 3; a++) {
            double x = triangleList.get(i)[a][0];
            double y = triangleList.get(i)[a][1];
            double z = triangleList.get(i)[a][2];


            double X = rx(x, z, Math.toRadians(xDir));
            double Y = y;
            double Z = rz(x, z, Math.toRadians(xDir));

            x = X;
            y = rx(Y, Z, Math.toRadians(yDir));
            z = rz(Y, Z, Math.toRadians(yDir));


            triangleList.get(i)[a][0] = x;
            triangleList.get(i)[a][1] = y;
            triangleList.get(i)[a][2] = z;
        }
    }


    double leastX = Double.MAX_VALUE;
    double mostX = Double.MIN_VALUE;
    double leastZ = Double.MAX_VALUE;
    double mostZ = Double.MIN_VALUE;

    double leastY = Double.MAX_VALUE;

    for(int i = 0; i < triangleList.size(); i++) {
        for(int a = 0; a < 3; a++) {
            leastX = Math.min(leastX, triangleList.get(i)[a][0]);
            mostX = Math.max(mostX, triangleList.get(i)[a][0]);

            leastY = Math.min(leastY, triangleList.get(i)[a][1]);

            leastZ = Math.min(leastZ, triangleList.get(i)[a][2]);
            mostZ = Math.max(mostZ, triangleList.get(i)[a][2]);
        }

    }

    mostX = (leastX + mostX) / 2;
    mostZ = (leastZ + mostZ) / 2;

    for(int i = 0; i < triangleList.size(); i++) {
        for(int a = 0; a < 3; a++) {
            double x = triangleList.get(i)[a][0];
            double y = triangleList.get(i)[a][1];
            double z = triangleList.get(i)[a][2];

            triangleList.get(i)[a][0] = x - mostX;
            triangleList.get(i)[a][1] = y - leastY;
            triangleList.get(i)[a][2] = z - mostZ;
        }
    }



    double[][][] newMesh = triangleList.toArray(new double[0][3][3]);
 

I tried first centering then rotating, but that did not fix the problem.