Proseal works great for this
Take some proseal put it in a ziplock baggie and cut a small portion of the corner off. Roll it up to compress the proseal like a cake decorating icing dispenser.
You can apply a nice even bead of proseal along the joint and the stuff can be painted if you want. I did this around the outside of the rear glass as well after masking off the window with 3M electrical tape. It makes a nice paintable fillet that blends the skin to the plexi.
Jeff - 120hrs flying -7A see you at OSH!