The reason they're blocked is because you want the coolant in the block to go to the back of the block before it goes up into the heads. Google search 'series cooling' for more info. The small holes that are exposed are to burp out air and help avoid air pockets that lead to localized boiling (fun fact: steam is 1600 times bigger than water).
The side effect of that is the front cylinders run the coldest and the front combustion chambers run the hottest. Some newer engines utilize 'parallel cooling' where a metered amount of water is bled upwards between cylinders. The science is to have a more even temp on the combustion chambers since you have to tune to your weakest hole.
What's odd is that your 4.1 block doesn't have steam holes between the cylinders on the low side. On my build I drilled my 8445's so the air could burp out on those areas since water can flow between the cylinder liners. It might not be a bad idea to seal up that deck and put a small hole there in the discolored areas before the heads go on.