Now I don't have my manual home, my brother has it, so I'm going to need some input back. Also, If I had my manual I could tell you the wires you need to hook up where, on both machines, so you will have to dig for yourself a little.
One, the CDI for the RXL should have these wires...
Black/Red
Green
Red
White/Red
White
This should be pretty much the same as the leads coming from the stator of the carb 650 motor. Let me know if I'm incorrect. Hopefully the connectors are the same.
Now, there is a difference between the RXL stator and the stator of the carbed 650. This being that the carbed version two of the coils are in series with one another.
So if you want you can put the wire the stator so they work independently or as one, but it will be more difficult as one, as you'll be changing the number of voltage regultaors you have in your system. Right now in your RXL chassis their should be two. My suggestion just wire them independently. I recommend this if you plan on keeping the EFI or even if you do not. So one of the coils will go to the rectifier, this being the coil with the Gray and gray/white leads on the wiring diagram. The other coil can have one side or should have one side grounded to the motor. Then the yellow lead on the coil in out wiring diagram can go to the other voltage regulator. You'll have to do some digging to find this stuff. One of the regulators should be by the relays and the other should be under an arm that comes out where the battery is. That should take care of that.
Now if you are getting rid of the EFI you can pretty much follow what I've posted above. Hopefully this helps. By the way, I believe the black/white still has to connect to the black for the killswitch along with the red or else you lose the spark. Maybe Polarick will chime in with a definite answer on that.