Ok..
Four wires setup is.
Green Right Turn
Yellow Left Turn
Brown Tail Lights
White is ground.
Having a three-wire setup means (I am assuming based on common sense) that you have a LEFT turn wire, a RIGHT turn wire, and a TAIL LIGHT wire. Which means you are picking the ground up from the trailer.
So,,, I am betting your old lights had a wire or somehow were grounded to the trailer.
Thus,, you will have to take the white wires from the LED lights to the trailer (White=Ground).
Now you will have to do a little guess or testing. Use a DVOM or a test light to confirm which is the left and right turn and then you can follow the wire specs I posted.
Or,,, look at the back of the trailer, I believe you will find two wires on each side near where the lights mount and or, one side will have three wires and the other side will have two wires. If you have the 3/2 setup, look at the color of the wire that is on both sides. This will be the tail lamps wire. Hook your TAIL LAMPS wire to BROWN.
This will leave one wire on each side not used. This unused wire will be the turn wire for the side. Hook your wire to the GREEN WIRE on the right tail lamp as this will be your right turn wire. Thus,,,, hook your left turn wire to the YELLOW wire on the tail lamp on the left side of the trailer.
Make sense...
If it were me, I would remove the three-wire system as it is the least reliable system out there. When you use the trailer as the ground you are doing and or having many issues.
1). The ball is the ground connection. If it is dirty or greasy it can loose it connection. Even if it has a connection at the full 12 volts, it often does not have a good enough connection to allow for the amps to do their job.
2). You are running electricity into the trailer which begs for electrolysis when it comes in contact with water. This promotes corrosion at a very fast rate. Which brings us right back to poor connections. As they corrode, the connections loose their quality contact, create additional corrosion, and dim the lights or they nor work at all.
If it were me, I'd buy a 4-wire harness and use it. MUCH better quality connection.
In fact, now that I type this, I changed over to LED's earlier this month and never used the NEW 4-wire harness that came with the lights. If you want it I'd sell it to you dirt cheap.
I will include a link to when I installed my lights. I suggest you SOLDER the connections as this further helps the longevity of the quality connections.
If you do solder them, I suggest using heat shrink as I have, don't forget to put it on the wire BEFORE you twist them together.. LOL
Here is the link, take a look at the connections...
http://www.seadooforum.com/showthread.php?63155-Installed-New-LED-Tail-Lights