Been awhile since I had a head off but typically the head contains large openings used for core cleanout from the casting process. The gasket usually has smaller holes to meter the coolant flow and to bleed air entrapment, this prevents coolant flow from "short circuiting" by not distributing coolant to the rear cylinders.

Coolant flow is typically front to rear in the block with larger passages in the rear reversing the flow from rear to front exiting at the thermostat housing.

The metered passages are usually a little larger on the exhaust side since obviously more cooling is needed here.

I would place the new gasket on the block and I believe this will all make sense.

Tom (Service engineer for Victor gaskets)

Some engine designs also have blank passages in the gasket to increase loading in that area.

I would suggest before you put it back that you take the head to a machine shop specializing in cylinder head repair. Sounds like it is warped. If it's not too bad it can be resurfaced and reused. They can also clean out those blocked cooling passages which probably caused the problem. The same thing happened on my 740 but it was too far gone to be repaired. The head gasket let go between cylinders 1 and 2. You really need to replace that antifreeze every year or so to maintain corrosion protection.