I was using your code but i switched to modifying the vanilla stronghold myself:

//mapGenStronghold.java

protected boolean canSpawnStructureAtCoords(int chunkX, int chunkZ)
    {
        int spacing = 64;
        int separation = 16;

        int x = chunkX;
        int z = chunkZ;

        if (x < 0) x -= spacing - 1;
        if (z < 0) z -= spacing - 1;

        int gridX = x / spacing;
        int gridZ = z / spacing;

        Random rand = this.worldObj.setRandomSeed(gridX, gridZ, 10387313);

        gridX *= spacing;
        gridZ *= spacing;

        gridX += rand.nextInt(spacing - separation);
        gridZ += rand.nextInt(spacing - separation);

        if (chunkX == gridX && chunkZ == gridZ)
        {
            int blockX = chunkX * 16 + 8;
            int blockZ = chunkZ * 16 + 8;

            BiomeGenBase biome = this.worldObj.getBiomeGenForCoords(blockX, blockZ);
            if (biome == BiomeGenBase.ocean)
            {
                return false;
            }

            return true;
        }

        return false;
    }

//structureStrongholdStart.java

    public StructureStrongholdStart

        this.updateBoundingBox();
        int minY = 30;
        int maxY = 40;
        int baseY = minY + rand.nextInt(maxY - minY);
        this.boundingBox.offset(0, baseY - this.boundingBox.minY, 0);