I'll suspect the condenser.
Sneezles61

I wish! I already replaced the condenser. thanks though, keep the suggestions coming!

yes, once I installed new points/condenser I re-timed the bike using a dial indicator and ensured that the points are opening/closing as they should. 

unfortunately I don't have the original ignition coil. so i'm left with just aftermarket options

Have you checked/set your plug gap to 0.020 to 0.024"? 

It's starting to sound like the scenario described where the source coil is acting up...  I've never had it happen to me but another member documented it pretty well.  I think he posted here earlier.

After points/condenser replace and re-time and still getting intermittent spark, the problem could still be either ignition coil or source coil. Others on this site have had good experience with the Emgo coils, so points to source coil, but not certain. You could try another ignition coil, but to be sure whether it is either, you should measure the peak voltage coming out of the magneto. The meter you show in your 1st picture only updates twice/ second (500ms). That is not fast enough to catch the spike from the mag. Perhaps you could borrow a meter (or maybe rent?) with a peak read function. You need a 1ms update to see the correct value from the magneto.

Also, clean NEW points by pulling strips of white tuft-free card stock (white uncoated business card) through them until it comes out clean. 

I've had brand new points not work...  sitting in storage an invisible layer of corrosion can form on contacts creating intermittent/no spark

Badly crimped joints or pad fitting connector blocks can cause problems too.

Old twin cylinder snow sleds... When a condenser starts to go... One cylinder, the bad one, won't run while it idles but the sled will run... Once you get some RPM's up, the bad cylinder starts working... I've found I need to take the condenser right out of the sled, and test it while sitting on a piece of wood... I doesn't take much to complete the circuit/grounding the condenser attached to metal... Very frustrating.. 
Sneezles61

Are points and condenser aftermarket or Yamaha?