well it can't be running at 180 out, that would mean the spark is happening at bottom center. When you used the ohmmeter did you wiggle the wires too make sure that there isn't a intermittent problem that doesnt happen under vibration ?heat?
double check wiring hookups clean/tight properly hooked up ,color coded ,grounds clean and tight. unfortunately the usual test for a cdi is that everything else checks out ok. usual troubleshooting flow chart for ignitions such as yours is No spark, check plug,check plug wire, check engine kill switch,check wiring/contacts and grounds,check resitance of coil,check resistance of stator,replace cdi
If the bike is timed statically right and it runs then the timing gets radically off the wall(easy to check with timing light and the ignition cover off) with rpm I suspect the wires arent hooked up proper or the cdi crapped out