I suggest that you do two things:
Open the boot on the sea chest side of the transmission oil cooler. This is inline the hose from the sea chest to the Yanmar water pump. Use a wet vac to suck all of the debris out of it.
Next, check the hose clamps at every connection between the sea chest and the water pump. Now would be a good time to replace them all. Do not tighten the hose clamps too tight on the transmission oil cooler body because the metal is soft and you will close the water paths through it.
I believe you have suction side blockage (most likely in the transmission cooler) and because of the suction side blockage you have air entering at a not-so-secure hose connection.
Please let us know if this guess on my part helps you solve your issue.