For the stringers, you want them suspended off the hull about 1/4 in. If they are in contact with the hull, the imperfect fit can cause "hard" spots which can cause cracking over time. After coating the bottom of mine with resin and letting it tack up, I suspended mine at the height I wanted and then pushed the pb under them. I used a gallon ziploc with the corner cut off like a pastry frosting bag to dispense it. Then I used a big plastic spoon to give the fillet a radius.
The added strength at the old to new stringer joint shouldn't be a problem.
For the transom, the pb acts as a glue to keep the wood and outer skin attached. It also fills any voids. If the wood and outer skin are not attached, there will be excessive flex in the transom which could lead to cracking. Although pb is the most recommended option, if the outer skin is pretty smooth you could use a different glue. Some have used PL premium construction adhesive, but it has a very long cure and off gas time (at least 72 hours or more). You could also use a layer of csm and resin. I would suggest you try and grind a bit to make the opening bigger, so it isn't such a tight fit. Some pb getting pushed to the bottom is probably ok as long as there is enough still there to glue it properly.
The added strength at the old to new stringer joint shouldn't be a problem.
For the transom, the pb acts as a glue to keep the wood and outer skin attached. It also fills any voids. If the wood and outer skin are not attached, there will be excessive flex in the transom which could lead to cracking. Although pb is the most recommended option, if the outer skin is pretty smooth you could use a different glue. Some have used PL premium construction adhesive, but it has a very long cure and off gas time (at least 72 hours or more). You could also use a layer of csm and resin. I would suggest you try and grind a bit to make the opening bigger, so it isn't such a tight fit. Some pb getting pushed to the bottom is probably ok as long as there is enough still there to glue it properly.