When assembling an engine after a rebuild, I coat critical parts with a thin film of grease such as Lubriplate or similar. I do not think the type of lube matters all that much ..... Just get some on the parts to prevent galling until the oil reaches them.
I do not think you can kick over an engine enough to generate the oil pressure and oil flow volume necessary to adequately protect the parts. I hope you did not assemble the engine "dry".
The primary case is not part of the engine lubrication system .... a separate oil fill is required. I fill my Atlas primary with 7 ounces of Ford type F auto transmission fluid.
The oil level should be just enough to touch the lower run of chain with the bike level. Add some oil, kick the engine over in neutral, touch the upper run of the chain with your finger thru the inspection hole . Add oil until your finger gets wet with oil.
The transmission is also self contained. Add oil up to the level of the overflow plug on the rear side of the gearbox. The type of oil recommended in the original Owner's Manuals was 50W motor oil, some prefer EP90 gear oil. We could start an argument over this. I think either type is adequate.
Slick