1973 DT3.  So I put the crank seal in on the primary side, and now I discover this Tusk Crank Puller/Installer has no fitting to pull the crank through  on the primary side. So all I know to do  is use the heat/freeze method, I figure that a torch on that he bearing will ruin the seal as will pulling seal out before heating the bearing.  But before I do that,  I thought I would see if anyone could think of a non-destructive way out of this predicament..

If you mean "clutch side", most of the time Yamaha had more of a "slip fit" as the crank is clamped to the inner bearing race when tightening the primary gear nut. 

I might just be super lucky but I've never had to pull the crank into the clutch side bearing. 

DEET makes (or at least made) a tool set with the correct adapters if you need it.

Yeah, it seems like after I split the cases,  the clutch side of the crank just pulled out by hand, notthing needed. 

So long as you already have the bearing in the case you'll be good & yep crank slides in & if not just a wipe with wet & dry paper. Designed to slide in. If on the other hand ya talking inserting crank complete with bearing ,& seal is already in, then different story. But I don't think ya mean that so all good.