Nice work on the transom and removing the cap. It's much easier to glass the cap back in place then to fair out the entire outside of the transom.
I noticed that you put a layer of glass on the backside of the dash and then used wood plugs to fill up the holes and then puttied over that? If that is the case then you will get cracking around were the holes were filled over time. The correct method is to grind a bevel around each hole and then glass up to the edge of the bevel. It's Ok to use the dowels as fillers so to speak however you need some glass over them for strength. Speaking from experience
strick