Polyurethane sealant like Sikaflex 291 won't need very long to set. In
reality, only a very small portion is in contact with water anyway as the
amount of sealant between the through hull flange and hull is very thin.
I'd allow about a day, but I live in the tropics, so cold weather might
take longer.
As for enlarging the hole, there are various "tricks" that can be used to
allow a holesaw to be used. One is to use a holesaw of a style that allows
two blades to be used together (I've seen these sold for installing handles
on household doors) - one the old size and one the new and another
technique is to fasten thin ply over the top and bottom of the hole and
then cut out the hole with a conventional holesaw.
Old through hulls can sometimes be a bugger to remove, but at that small
size shouldn't be a problem. If you look inside the through hull, you
should see a couple of tangs. I usually cut up a bit of steel flat bar to
make a tool that jams against the tangs so that it can be held fast with a
shifting spanner while the nut is undone (or done up in the case of a new
installation). Quite often they'll need a whack with a hammer to allow them
to break the old seal and drop away from the hull.
As for the two layers, don't worry about it. The thickest layer is the hull
and the thinner is just the glass used in the making of the engine bed. On
my boat (a series 1) there was a thin layer of grey filler between the two
layers. The polyurethane sealant at the flange of the through hull will
stop any water coming in, and the nut on the through hull when tightened
will keep the layers compressed together.
One thing I did was make a plywood "donut" of about 2" outside diameter
that goes between the hull and the nut of the through hull. The donut is
coated in epoxy and the polyurethane sealant used to glue it to the hull.
The purpose of the "donut" is that it provides extra rigidity for the
through hull mounting and also improves the seal of the through hull to the
hull by evening out any differences in thickness and "bumpiness" of the
hull at the mounting point (remembering it is actually slightly curved
here).
I also didn't worry about an outside strainer, as I've heard stories that
they can prevent access to the through hull if it needs cleaning because of
marine growth. I use an internal strainer instead and have it set so I can
remove the intake hose and run a rod down to the through hull if it ever
gunks up.
Anyway, I'm waffling on now lol. I don't have a picture of the actual
through hull set up, but here is a picture of my installation:
