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Actually, thats not right. A big block has two waterpump holes at each side of the block(r&l). Water does flow into the block from the lower hole, around the cylinders,(and normally thru holes in the deck to the heads in small quantities) to the back of the block, where it enters the head and than flows back to the front water passage, into the front of the block. The front water passage in the block is separate/divided from the inlet waterflow. Remember, a big block has the t-stat housing on the pump, not the intake.
The picure shows the upper small holes in the deck, but on a siamese block, air gets trapped in the hourglass shape on the lower deck because the air cant escape between the cylinder bores. Your gaskets will have holes in them, and my guess would be that your heads have holes there also. It may be as simple as drilling a few 1/4"holes in the deck to get rid of this problem.
The timing you report seems awfully low. Do you have a real small cam?

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My heads are Indy 440-1's and yes they do have the lower holes (see pic, see the two lower holes shaped like arrows).

My cam is very small. Intake duration is 224 degrees at .050 and lift is .541 and Lobe Sep Angle is 116. The ignition timing is so low because this was the first time we put boost in the motor and we wanted to start very conservative on the timing and a/f and then creep up on the tune to make more power. On that pull we only put 7 lbs of boost in the engine and it only made 707 hp at the wheels. Figure it would have gotten closer to 800 whp on that boost if we could have run more timing and leaner a/f... but as I said we only got the one pull in on boost and burned those two pistons.