Cant get rear wheel back on

Putting the Axel in backwards, so long as you have all original spacers in place, in itself won't make any difference regarding the awing arm.
BUT, the head of the axle has a slight taper where it pulls into the diff housing, having this backwards wouldn't (shouldn't) cause your problem, but it is not correct.
 
I was thinking maybe all the threads on the axle are used if its backwards but not if its in right?

It doesnt seem like the wheel is on they way it should be, but maybe it is and my swingarm somehow got bent in. I can post a pic to show what I am working with. I cant think of any other reason it wouldnt go on as it did when I first had the bike.
 
I always have a bit of time wrestling the spacer, caliper bracket, and caliper all into place at the same time.
I haven't found a trick to it yet either. Just lift, push, pull, shake then try again.
Finally the planets will align and she'll ease into place like I knew what I was doing.
One thing is for sure though; it's not going anywhere if the differential isn't seated well.
 
Dont know if this will help, but its how I do it....loosen the 4 acorn nuts on the drive unit, fully assemble everything in place, then retorque the 4 acorn nuts (btw, I blue locktite mine).