It starts up with the old cdi.

 

Still stalling when warmed up? Did the reverse light issue go away?Did the plug in for the cdi seem ok, not loose or coroded?

 

When I put the old cdi in it in starts up but still stalls when warm.

 

Then youre back to doing more troubleshooting.
Do you have a ohmmeter? Did you check the resistance of the stator coils? Did you recheck them when the motor stalled?
It could also be the wiring harness, like the other guys have said. Youll need to look over the connections, and plugs, and maybe wiggle them while ohming them out, looking for intermitent connections.

 

the 250x and 300ex cdi's aren't compatible. the 300ex is a DC unit, and the wires in the harness are different on them. your problem does sound like a possible stator though. the specs in the honda manual are 100-300 ohms between the black/red wire and ground for the stator. try to measure it before and after it stalls. bad stators aren't all that uncommon on the 250x's. also check the connectors at the coil, i had a wolverine act up after 5 minutes of running, it would cut out like it was starving for fuel. turned out to be the primary wire on the coil was loose and corroded, cleaned it and tweaked the connector, and it was fine.

 

I put a OEM cdi on it and it runs fine now.