Chris, without knowing exactly which type of exhaust system you have, I'm going to generalize this since these are all basically very similar with regard to the sea water flow.... I.E., log style w/ rear elbow, or center-rise.
On a typical Raw Water Cooled Marine exhaust manifold and elbow (aka riser) we'll see several ports between the manifold and elbow.
The large port will be the main exhaust port, and the smaller ports will be what some of us call the "sea water transfer ports" or "spent sea water transfer ports".
Queston: When you say that only the round hole was open, are you talking about the main exhaust port, and that the transfer ports were closed off?
If the transfer ports were closed off, then typically the manifolds will be supplied and also offer a sea water outlet.
This means that sea water enters the manifold at one area, and exits the manifold at another area.
Only after the sea water has entered/exited the manifolds does it find it's way to the Elbow or Riser.
In many cases, the sea water that has exited the manifold, passes throught the T-stat housing prior to making it's way back to the elbow.
This one shown is a center-rise, but if you'll look at it schematically, it may be very similar to a log style.
Note that the gasket transfer ports are closed off.
The transfer ports can be completely blocked off.... or some will be blocked off, yet have a small weep hole in them.
None-the-less, if this is the scenario (in and out of the manifold and then onto the elbow), and if you were to now install gaskets with fully OPEN transfer ports, the system will become unbalanced, so to speak.
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Now.... if the manifolds are fed at one end ONLY, and if the transfer ports are used to feed the elbows, then these transfer ports within the gaskets must remain open.
Here's an example of a center-rise exhaust manifold that uses a single supply.
Note that only one transfer port in this particular gasket is open.
However, it is just as common to see two and/or all four gasket transfer ports open. (some will even have six transfer ports)
If you could post photos of your exhaust system and hose arrangement, we'd be better able to help you.
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