bcobbet,
I also live here in Saint John. Lightening holes are just sections cut out. You would drill large diameter holes with a hole saw and then connect them with a jig saw. You would only do this one sheet and only in places where you did not need full strength. This will allow you to put more weight and strength where you do need it, like the edges, and gussets, and where the motor mounts. You might also be able to reuse the pieces you cut out somewhere else.
I am not sure if you are also replacing the floorboards and gussets. They look like more plywood over to of the aluminum. If they are dried out and in not too bad shape you might be able to get some more life our of them by getting them to soak up some epoxy. There is epoxy specific for that purpose but regular epoxy will do also. You don't want to use too much as it is expensive, but it also bonds well to the aluminum, if that is what you want. Best time to apply epoxy to wood is after the wood has heated up, like in the sun, then move it into the shade and apply the epoxy and the cooling wood will suck in more epoxy that way as some of the water vapour in the wood condenses. A hair drier will work also. The wood should be as dry as possible though. I wouldn't mind taking a look at it over a beer if you want to PM me, just to make sure I am not steering you in the wrong direction. I live in the North End.