MB,
For the transom, I would do all 3 layers in the same day.
Wait for the 1st layer of mat to set to a hard tack, so you don't diSturb it and create air pockets. Next, lay down the woven roven. This will soak up resin like it is going out of style. When this sets up lay down your final layer of matt. If for some reason you can't do all 3 layers in timely fashion, then lightly scuff the cured suface with sandpaper and wipe it good and clean with old rags soaked with acetone.

I don't have a clear picture in my mind of your stringers attaching to the transom. Use some bondo to fill inside corners to a curve. A tongue depresser or quarters work good as tools. Sand it fairly smooth. Lay down a few layers of 1 1/2 oz matt. Don't be afraid to tear it up to get it to cover the whole connection. You can then use strips of woven here, but it will not be easy to bend a short strip to an inside corner. Hopefully you will have an easy curve to the inside corner from all your mattwork. Fill in and top off with more matt. Whatever you are gonna do inside the stringer at the transom connection - do it before you glass like this, because you ain't getting back in there without a fight.