I'd suggest starting with the rear wheel and making sure the line of the drive chain is in line with the gearbox sprocket, then add the clutch and primary chain and see how this lines up. No need to tighten the clutch nut, a light nip will do for now. Chaincase can be left off to enable a good looky.
Somewhere on the forum this has been done in great detail, from memory Chaterlea John did some measuring. Maybe the authors can post a link?
As stated, the primary inner can flex, so worth checking it is straight, a homespun spacer or washers are often necessary to bridge the gap between the frame lug and the lower mounting down by the S/A pivot. The case should not be under any strain.
Any mis alignment in the front downtubes, mounting lugs and engine plates can result in a twist to the crankcase, so it is better to leave mountings slightly loose, get things aligned, then tighten the fixings.
Swarfy.