Dale the Builder has a big heavy boat with a 115 Yamaha on it. Put it in the water over the weekend and it runs and goes but it's not making any water. Nothing coming out the cooling drain.

Assumed (and you know how that works) it was a bad impeller in the pump, broken pump housing or plugged intakes/exhaust.

Dropped the lower unit and disassembled the pump and it looks like new. Impeller is good, tight on the driveshaft, gaskets are good, housing is good, intakes are clear. Reassembled (twice, didn't get the shifter spline in the socket first time...) and I can blow air in the outlet and hear it in the intakes and likewise blow air in the intakes and hear it in the exhaust.

Don't have water at the shop nor hose boots so couldn't run it. If the owner has hose boots we'll haul it up to the house and run it. If not he'll have to launch it and see if it's magically working.

Anything I've missed?

More info needed. Is it a jet or prop. A lot of times mud daubers build a nest in the pee hole. Take a piece of wire of something and poke to see if it is plugged.
Is it a two or fourstroke?

Two stroke, prop.

Where would the pee hole exit at? I ran air through the hole just below the hood in the rear, about 1/2" diameter. Thought that was the cooling water exit.

There should be another hole on the left side just below the cowling near the rear. It should be about 1/16" diameter; push a piece of string trimmer line up into it; it's often plugged w/ any manner of debris. You will, however need some water source to run it and determine if the line is clear. It's the last (and least important) place cooling water exits. Commonly called the 'pee hole', but a bit more properly known as the tell tail.
s.

Thanks, found it, reamed it (got some muddy water out) and blew a little low-pressure air into it and got water out the lower unit. Pretty sure that was it.

Yep, that should be the fix hopefully.

Anytime you first start the motor on any trip make sure that hole is peeing water.

He put it in the pond this morning and we have water!

Thanks for the tip!