G'Day Tilly... Yes there are variations in the type of drive sleeve, some run directly on the oilseal, others (like yours) have the distance piece spacer. In this case the drive sleeve is shorter, but the overall length is the same as the one piece drive sleeve with the smooth oilseal track. Assuming you have the right parts, assemble the spacer onto the crankshaft with the inner chamfer/internal taper towards the flywheel. This will allow the spacer to clear the change in diameter on the crank, and press against the inner race track of the main bearing. Assemble the drive sleeve and big nut onto the crank and tighten the nut, pushing the drive sleeve and spacer against the inner race. This will ensure the inner bearing race is seated against the flywheel cheek. At this stage there should be only the very slightest amount of end float on the crank. If it moves in and out at all you have a further problem to address. There is lots of information on the forum about finally assembling the cush drive and the need to tighten the big nut trucking tight.
Chain misalignment can be usually down to the variable pattern part quality of the clutch adaptor on the gearbox mainshaft, incorrect assembly of the gearbox is unlikely, but distorted mounting plates and incorrect gearbox position are possible. After all the time these bikes have been around mis matched, damaged, abused and spurious parts are to be expected. Luckily for you, the parts diagrams are available on this forum via the main header page. Haynes is a reasonable start, but does not have the depth of detail we sometimes need.
As Musky says, as long as the chain does not foul, your quickest option is probably a custom spacer.
The earlier plunger engine has the same dimensions on the crank splines, but has a completely different duplex chain, drive sleeve and cush drive/ sprocket and clutch assembly from the swing arm. Plunger gearboxes have a splined mainshaft in contrast to the tapered input mainshaft of the S/A box.
Swarfy