So what side of the crankshaft does the o ring go I'm thinking the long shift side right side. Parts diagram shows opposite side. Also manual stated insert shim when installing crankshaft, I don't recall a shim and parts diagram does not show a shim

Oring goes as in the drawing. Gear has a recess that traps it & squashes it to seal on the shaft
With the shim, if none came out of yours & none shown here in the pic then i'd go with that. Think those motors had a slight step to allow for not having a shim.
See what others say that are more familiar with the 400.

images.cmsnl.com/img/partslists/yamaha-d...gyau1068a-6_f384.gif

www.cmsnl.com/yamaha-dt400-1975-usa_mode.../partslist/A-06.html

Shims can get stuck to crank or bearing by "stiction", not noticed, and then lost. 

I'm not sure when the 400 went to no shims but it would be good to trial assemble by slipping the crank into right side case install the gear/spacer and snug the nut.  If crank had and needed a shim and it's missing, normally the crank will rub on the case when nut is tightened.  Best to find this out before final assembly! 

Don't ask me how I know!

If you need a shim, DEET might have them. 

& the conrod should be in the center line of the cases or close when assembled although the shim thickness wouldn't make much noticable difference to 'that'-- if it has one.

O ring goes on the right, on the inside end of the drive gear off the crank. I just used the same shim that was in the bike to begin with.