Re: Rebuilding Transom and Stringers...
I think the 'wrong' mix of poly resin & filler was used. Although Cabosil & resin will make a filler, it is 'thin' and better suited to filling small areas: chips and dings, not large, deep & wide areas adjacent to the transom ply. Typically, 'hairy' PB is used for structural applications, and filleting the transom ply would definitely be structural, IMHO.
I would remove the filler in the areas that cracked as best you can, completely would be best. Make structural filler w/ chopped strand, cabosil & resin and redo your fillets.
Save your fiberglass scraps when you glass other stuff. Cut it up into small 1/4" +/- pieces of chopped strand and use them to make your fillet filler.
You may want to try & make smoother fillets when you do it this go around, nice, smooth curve to allow the glass to roll up & over them should make the transom glassing go much easier when you do the tabbing & the follow up layers of glass out on to the hull sides.