Alignment between front and rear. Spindle seems to go in ok. I will have a look at it again as bik3rdude suggested and see if it possibly is a bent form problem.
Ok, if the spindle is going in as it should the forks shouldn't be bent. The wheel centres should be in alignment, remember the rear is wider the the front so when looking front to rear there should be an equal proportion of tyre down each side of the front tyre. Best way is a long straight edge clamped to the rear, with the front
wheel straight the distance between the rear/front edge of the tyre should be the same from the straight edge. Don't use the handle bars as a guide as the top yoke, the bars or both could be twisted or bent.
Start at the back, is the rear axle set to the same length each side? The marks are a guide but aren't always correct, measure from the centre of the spindle to the end of the swing arm, the line where the end cap which holds the adjusting nut. Once correct then check front to back and unless the rear swing arm or frame is bent (more on this later) the problems at the front.
It's possible the top/bottom yokes are twisted, the fork stanchions should side up through the bottom yoke and into the top without any problem, if there's any resistance or they require any force, the yokes are twisted and will need realigning. This would suggest some kind of front impact, have you hot anything or dropped the bike?
If the wheels are aligned but the handle bars are no longer square either they're bent or the top yoke is twisted.
If the yokes are fine and the rear is fine and the wheels are still not aligned something is bent. This could be, the head stock, frame or swing arm, has the bike had any frontal or rear impacts that you know of?