OK, after looking at the 7-way diagrams at
http://www.etrailer.com/faq-wiring.aspx it seems your trailer is using the "RV standard" but the new cord is using the "Traditional" standard. This explains the brown-green and green-brown swap. When you originally wired like colors, that's why your right turn signal flashed the markers.
Anyway, I still think your marker lights may be the "unknown" green/white wire which makes sense considering the RV standard is green for marker and tail. Connect that with the other trailer green (brown on truck) and it should work.
The bundles of wires under the wire nuts (twist locks), are probably ground and battery positive. If your truck has a charging circuit you can probably connect truck side black to the red bundle. Before you do that, confirm there is +12V on the red bundle with the trailer disconnected from the truck. Did the old cable have red and white wires connecting to those wire nuts?
The original solo yellow wire was from the truck 'aux' or reverse lights and was capped off since the trailer didn't use it.