when he rewired the harness did he plan on using a 06 r cdi or was it wired for the 06er cdi?
on the er cdi you need to add a condenser and power the safety circuit side of the cdi,
post a schematic of exactly how its wired and I will be able to tell the issue

starting and dies sounds like you need a condenser to power the ER cdi.. that's the symptom it makes

the red ricks cdi doesn't need the carb safety circuit power to start like the er cdi does.. but your better off with the oem cdi wired with condensor