When you place the rear wheel back on its splines it should sit there quite happily. If it doesn't then it means that it isn't on correctly. It is easier to put on if the bike is in first gear as you can wiggle the wheel as it slides in. Once it is on the splines then you feed the axle bolt in from the LHS. You will have to line the spacer and the brakes up and jiggle the wheel a bit as you then feed the axle through those bits and eventually through the swingarm. It is tight, but it will fit.
When you put the bolt that stops the brake callipers from flying around the axle back in, MAKE SURE THAT IT GOES THROUGH THE HOLE THAT IT IS SUPPOSED TO GO THROUGH ON THE SWING ARM!!! A couple of bikes at a recent get together had them wrong - and the work was done by a dealer!!!
While the wheel is off, did you remove the final drive unit (diff) and grease the splines? That should be done on every tyre change, and more often if you run on the Dark Side.