Ok Brian, here's how you can do it. Though some of what you've got you won't use.
First off ditch that automotive module pictured and mentioned above. Instead get a Badlands ILL-01-A .
http://www.badlandsmotorcycleproducts.com/2008/Products/BETCSM.htmEven though the trailer has dual filament 1157 bulbs in the corners you won't use both filaments. Only the bright brake light half of the bulb. In other words you'll be using it like an 1156 bulb.
That Badlands module will combine the tail light, turn signal and brake light functions on to a single wire for each corner. That's how you'll get everything including a separate dedicated brake light feed in a four wire plug. Do this:
Under the saddle plug the Badlands module in BEFORE the trailer harness pigtail adapter that you've got. You can then use the trailer pigtail's right tail light and left tail light wires to feed brake/run/signal to each corner of your trailer. Remember to use only the bright filament of the 1157 bulbs in the corners of the trailer.
Use the ground leg coming out of the pigtail to be the ground all the way to the rear. Those three wires will now ground the trailer and get all three functions to each corner of the trailer (thanks to the Badlands module).
Now find the wires in the trailer pigtail adapter that are the dedicated brake light feeds. Since it's for a bike application there should be one for each side. They'll both be all brake light all the time. So it won't matter which one you use. Pick one and let it feed the third brake light in the middle of the trailer.
Voila, all functions on each corner and a dedicated third brake light all on a four wire trailer connector.