You are continuing to go great work--what energy!!!
You will find all of the hatches--and the forward deck hatch while you are at it. Even the only new boat (255 Tom Cat) had wet core from just the wash down around the forward hatch. I pulled it--and found that half of the screws didn't go into the deck--the cut out was too large! I had to dry out the core, cut it back, seal it, and then add about 3/16" of glass all around the cutout!
All of the back hatches leak--there is a hatch which will fit the cutouts which is water tight--and that is what you will want to put back on. I don't have the number right at hand, but if someone doesn't, I'll look it up, and put a photo from my album.
For small areas of non skid, I have gel coated very thick, then used a Dremel tool to cut new non skid after laying out the pattern with pencil. Most areas you cannot see the difference. For larger areas, the areas as in the link are the way to go. You can roll or brush on the PVA, it does not have to be sprayed. That technique works particularly well if you are molding a new part. You can make a panel, and then cut out what you need also...
I would just cut back any obviously rotten core on the gunnel and then seal, fill and finish as you wish. A wooden plug for where the rod holders will work, put wax paper under with either a support, duct tape or even hot glue to hold until it has set up--then circles of mat and cloth to build to where you want to start the gel coat. There is no real structural strength there, so you don't need to feather in the edges on the 12/1 ratio. Another possibility is to put teak step plates over where the holes were. There are also framed rubber step plates which were used more in wooden boats, but would work to cover a defect where the rod holder was.