Did you ever try cleaning your points?

With a good ohmmeter, preferably an analog (swinging needle) type with an Rx1 scale, you should get 0 ohms with points closed and about 1 to 2 ohms with points open.

So with the points closed, scope should read no voltage. Components are precisely placed on the stator so that points open when voltage generated by magnet passing by stator coil winding is at or near maximum.

That sudden surge of voltage when points open energizes the primary winding in the ignition coil in a split second... the sudden creation of a magnetic field in the ignition coil primary winding induces the high voltage in the secondary winding of the ignition coil and Viola! Spark!

(Ignition coil is just an AC transformer)

You might do a search of my post on CT2 175 ignition problem, I took scope readings and posted them there. Mark is correct about points as well. If they they do not electrically contact,(0 ohms when closed), you will not get the proper saturation of the coil needed to generate the "spike" to the ignition coil.
alnarv

Have you checked your ignition coil to see if it works? Seems like you have checked everything else 

To reply to both you and MarkT, where are you guys saying I should be reading this? I have been measuring between black wire and ground this whole time, is this the correct place to be checking? I have also been checking it with a lower end multimeter. In the same lab that I had the oscilloscope, however, I do have access to a very very high precision benchtop multimeter where I could check with more certainty. What it's looking like is that I might go back to the lab again and redo my readings, since the one kick reading I have shows a potentially concerning picture. Also I suppose I haven't actually cleaned the points because they just look really clean, but I can give that a shot too. Come to think of it, when I said it didn't run most recently, I have just now realized that I still had tape on the points. I might actually go outside in a moment and take that off and see if it has spark now. Anyway, your input is as always appreciated. Let's hope for some good news soon!

Also, additional question, does anyone know if these voltages are typical for these coils? Thanks again.

Have you checked the tire pressure?
Sorry............couldn't resist.Keep at it,I've been there.My bike's a screamer now and starts first kick.

www.dropbox.com/s/9gink72q15lg76r/Photo%...3%2058%20PM.jpg?dl=0

This is from my CT1C manual it shows you the test process also clean your points Really good since you had tape on them could have some glue on them be sure to take the plug cap off if you do the test 

I still think that if ya getting spark by spinning it with a drill & not at kick speed then source coil just isn't making the volts. [If i'm on the right page--& all the oscilloscope stuff is beyond me lol]. Sorry if i'm not keeping up.

There waw a lot here and i breezed through it pretty fast, but one if the things I noted was you mentioned a CDI ignition. Realize that the 73 DT3 was originally a points bike. If the bike has been converted to a CDI ignition, has it been done properly?

If it has been converted to a CDI, the manual will be somewhat helpful, but the measurements and readings are for a points based bike. Be sure to account for the differences in the CDI ignition if this is the case.

Ha yes i must admit i do that & skip through long post trying to pick out important bits and i remember that cdi coment burried in there way back but think he was reffering to the condencer so should be good. I write blimmin long essays too that tend to wander off course at times & hope the message gets through.

The Energy transfer magneto design that Yamaha used on these Enduros has been called a "mechanical CDI" .