Please note, that it will take you kicking the engine over, to at least 750 rpm for the stock 250R ignition system to even produce a spark. That is if the system is in good shape. On the 250R stock ignition, 9 out of 10 where theres a spark problem, it is either the wiring harness connectors, or either the connectors up inside the plug on the CDI box.
The black wire with the white stripe in the harness, is the main ignition wire, check that wire in the plug going into the CDI box plug. Try bending the harness around at the CDI box & tie wrap it to the box, put that plug in a bind & a lot of times you'll get spark back.
Think of it like this, all the times during that ignition systems life span, that it has been pulled apart & pushed back together during a rebuild & how much stress have been put on those connectors, wires & little male pins in that plug on the CDI box.
Over time, the male pin for the black wire white stripe, it can be broken loose inside the CDI box & you can have intermitted connection from time to time depending on how much pressure put onto the plug hooked up to the box.
There were two members on Mac Dizzy.com, that were the 250R ignition gurus, ol Teamgeeks 6 & Ramajacoony from South Africa. They really dug into the 250R system & found its faults & how to correct them.
Neil