Motorcycle Repair: 81 Yamaha XS650 with no spark, key switch, xs650

Question
She was running two days ago but the battery was weak.  I went to charge it and the positive clamp from the charger touched the frame (both positive and negative clamps were attached to the proper terminals). There was a big spark and the clamp was actually "welded" to the frame. The lights and the starter work but now I am not getting spark from the plugs.  I am certain something is fried but I am not sure where to start looking.  I have tested for continuity and everything seems fine in that regard. I am a novice and I just bought my first multi meter today.  What would you suggest?  Thank you.

Answer
have you replaced all fuses yet ?
if so do continuity checks thru the key switch and rt handlebar switch on the ignition circuits...you will need a wiring diagram,and a manual has this in it.... make sure though...

The ignition ignitor unit could have been damaged , especially if the key switch and rt handlebar on/off switches were on...can you try a used ignitor, if new fuses don't do it ?