I always make sure those two holes are blocked-off. On race engines I thread those holes in the block's deck and install plugs.
http://www.slantsix.org/articles/dutra- ... ckquiz.jpg
Think about the coolant flow, cold coolant enters the water pump and goes into the front of the block at the w. pump flange. The coolant travels to the rear of the block picking-up some heat, but not a lot.
The coolant then passes up to the rear of the head though those 2 large holes at the rear of the engine. At that point it travels forward through the head where it picks-up most of it's heat.
Note that the block and gasket has 6 small 1/4" "bleed holes" that allows a small amount of the colder block coolant to come up into the head, right under each exhaust port. This helps keep these super hot areas cool.
If you open-up the 2 holes in question, you allow the colder block coolant entering the block to "short cut" right up to the front of the head and back out of the engine. The bad news is that this "fools" your temp. gauge into a low reading, that front hole allows a lot of colder coolant to enter the head right under the sending unit while the reduced pressure / flow to the rear of the engine runs the rear cylinders hotter.
Bottomline, my thinking is that you never want to unblock the front hole and in most cases, also keep the center hole blocked.
I do talk to some people who say that it is helpful to partially open the center hole. (5/16" hole) The thinking is to help even-out the head temperature by adding additional cold block coolant to the head at the mid-point. This makes some sense seeing that the front of the head does see the coolant when it is the hottest.
DD
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I think I will just run this gasket until I have a chance to play around with another head and do some porting. Hopefully taht won't be too long and hopefully no damage will occur. 
