I don't see why you couldn't run a XR600 CDI, but it will take a lot of changes. First you will need a XR600 stator. I have held both a XR600 and a XR650L stator but not at the same time. If I remember correctly they are more or less the same size. You need the XR600 stator because it has the high voltage exciter coil that powers the CDI. If a XR600 stator will not mechanically fit, you can forget this idea. That exciter coil puts out over 100 volts when the engine is running. About 60 or so volts is needed to produce a spark good enough to start the engine. A stock XR600 stator might not have enough of a lighting coil to power the headlight and recharge the battery. A high output stator would be a good idea.
The pulse coil on the right side of the crankcase is a different part number between the two bikes. It might just be a different connector, or it might have different electrical characteristics.
The ignition coil is the same part number between the 600 and the 650L. No worries here.
There is a lot of wiring harness hacking that would need to be done in order to get this to work. The 650L regulator would have to go and be replaced with a dual sport kit type DC regulator. The connectors on the XR600 CDI are pretty specialized. The easiest way to get one would be to get an entire XR600 wiring harness and use what you will need to connect everything.
I actually swapped between CDIs a few weeks ago - the plug is the same but the wiring is different so I had to pull pins - it was like wiring a bomb!!!
But I did it - they are both very simple CDIs - they need power and they need to send the signal
I could do the pin out for you guys to show you the relativities.
Of course I run essentially 600R architecture - stator plus flywheel but I also run a 650L regulator just to confuse you!!!
My bike is very much a hybrid.
Bottom line is atm I cant estart my bike with the 600R - 10 minutes and a quick rewire to accomodate the 650l CDI and I get it back but I lose big power.