Ok you installed new spark plugs during the rebuild.
Now with the problem did you check with an other new set of spark plugs to see if the problem still exist?
How much is the battery voltage,did you check it with a multimeter ?
To check the coils you need a multimeter to measure the ohm resistance.
Read Dave Ett's post here about how to check the coils http://www.nsr250.net/forums/viewtopic.php?t=11280&highlight=coils+check+cheque
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