The larger hole to right and near the bottom is for a drain plug.
I don't think it's original...but maybe.
Is it actually flush with the hull bottom? It looks kind of like it is raised. That would make it difficult to get all the water out.
As far as the other anchors for the straps near the dagger board, that is going to be a little more problematic as an inspection port will not be really an option. Could I drill out the holes bigger and fill with epoxy/shredded fiber and drill new holes?
Why couldn't you put inspection covers on the top of the seat-like structure where the daggerboard trunk is? The main problem with inspection covers on top is that they are not strong enough to step on. If you really don't want to do it that way I suppose you could do a variation of a drywall modification.
Suppose you want to attach something to drywall that is heavy? Screws would pull out. So, you cut out a square of drywall. Then you cut a piece of 1" thick wood (like a 1x4 or 1x6) to go behind the hole that is longer than the hole. You put glue on the edges facing out, slip it into the hole and then place it with the glued sides touching the backside of the drywall. You can use a temporary brace to hold it there. Something like another piece of wood across the front with string snugging them up (like a clamp) works pretty well. If you are more impatient you can try something like liquid nails. Then you put the cutout back in place and repair the kerf. A lot of times you need to bevel the edge a bit to get enough room to get spackle in the groove.
So, let's say you were going to do something similar. If you got some aluminum stock like I bought that would make a fairly good backing material. You could possibly cut out a hole and then cut a piece of aluminum longer than the hole is wide. You would glue it to the back of the hole with thickened epoxy. You can thicken it with either fumed silica or wood flour. Sometimes sawdust will work if it is fairly fine. You can even try saving the lint out of your dryer to use as a thickener; that works similar to milled cotton (which was used before we had fumed silica). If you have never seen fumed silica it is like petrified snow. It is white and light and fluffy like snow but you don't want to inhale it or get it in your eyes. It takes a bit of work to get it mixed up in the epoxy.
If you don't have epoxy then if there is a boating store near you they probably have West System which is a good epoxy. If you have to order it I would get it from Raka because they also have a good epoxy but theirs is a bit cheaper than West System. The commonly available resin in car parts stores and most building supply stores is polyester which you can't use. Polyester has a very small container of MEK hardener that is added a few drops at a time. Epoxy harder is usually a 1:2 or 1:3 ratio with the resin so it is a much larger container. I would not buy an off brand at some place like Lowes or Home Depot. I bought an epoxy at Lowes that was labeled as Marine Epoxy. The first batches I did worked okay but then the next year it wouldn't harden. The manufacturer told me that the product was too old. That's ridiculous. Good epoxy should still work even after setting around for years. As I recall, the Raka epoxy I'm using now was bought seven years ago and it is working fine.
While you have the hole cut out you might be able to take care of the opposite side first. You can just use locknuts with washers or you could also use an aluminum backing piece.
Then on the hole side, once you have a piece of aluminum stock glued to the back of the hole you can replace the cutout piece. You might want to put thickened epoxy on the aluminum so that it is also glued to the back of the cutout piece. I would bevel the front face to make the cut wider and then put strips of fabric in to build the material back up in the groove. When working vertically it can help to use thickened epoxy so I would again think seriously about getting some fumed silica. You can't skip the fabric because thickened epoxy by itself is much weaker.
Now with an aluminum backing piece in place you can drill a hole and use toggle bolts if you want. You know that the aluminum can take the stress. The aluminum stock in the picture is 1 inch wide but you would probably want something wider to be sure you didn't drill off the side. The bolts will be loose in the hole because of the size necessary to fit the wings. They probably won't move much when snug so You could try just putting some caulking in the hole before you tighten it up.
As far as the rub rail damage and other where it will be hard to get to the back what do you think? Just grind away from the exterior through the gelcoat and layer with fiber/epoxy? Some instructions I have seen say to use glass fiber with some kind of mat sewn or something?
I'm not sure if you are talking about the material or the repair method. Mat is thick and stiff. It's good for building up but it won't bend. You need woven glass fabric. If you have a small gap you can just put strips of glass fabric in. If the gap is larger then you need a backing piece. Typically you use a piece of cardboard (larger than the hole) with a layer fabric over it. Then you run two strings though it near the edges. You wet the fabric with epoxy and then slide it inside the hole. You use the strings to hold it up against the back. After the epoxy hardens you have to trim off the strings and then you have a backing piece to lay the next layers of fabric on. Again, you normally bevel the edges so that it gets wider as you come out. This gives the edges more surface contact but it also helps the patch resist pushing in since it would be wider than the hole. You build up as many layers as you need to match the thickness.
Are you familiar? Stuff I found at Menards was just the epoxy with hardener, and a sheet of fiber. Is there another kind?
I would look here: Raka, Inc. 772-489-4070, Epoxy-Fiberglass-Carbon-Kevlar