Do you have a multimeter? If so check the wires that enter the rectifier (this is the pickup from the alt), if they are in spec then go on to check the output from the rectifier to the bike. If the problem seems to be the alt check its not the pickup itself is damaged (physically check and check the resistance).
Do these with the engine running and the battery disconnected (take out the fuse). You may notice the voltage under expected at idle and slightly over if you give some revs that's not a huge concern unless it's massively out of spec.
