Having issues with my chain... It was loose a few weeks ago, so I tightened it and it was perfect. Then it gradually loosened up, to where I could hear it slapping when I was slowing down. I figured, okay, I didn't torque the axle nut to spec (even though I swear I did), so today I retightened it, double-checked the torque on the axle nut, then made sure the axle adjustment nuts were tight (which I didn't do last time), and it was perfect, with about 1" of free-play, maybe a little less. I ride 20 minutes going 55mph and get home, and when I go to clean my chain, I find that it has almost no play up-and-down... for some reason, now it's way too tight. Gonna redo it tomorrow, hopefully all goes well? any ideas?

Also, how do you guys align the axle? I tried today using a small measuring tape and measuring from the swing-arm covers on each side of the chassis to the middle of the respective axle nut, but it still seems off - my rear brakes make a rubbing noise now when I'm at slow speeds, like the wheel is off-center and rubbing the brake pads on a certain part of the rotation.

I just "eye-up" the rear tire alignment........

As for the chain, sounds like you have a tight spot on a few of the links......did it sit for a while?  Easiest to just get a new chain.

I had the tight chain problem once.  Re-adjusted and it never came back.  Was nervous since i was about 300 miles from home.  That chain was tight.  Almost no play.

Try re-adjusting and torque to specs.  One way to tell if it's aligned is to either "eye" it, or count the threads on the adjusting nuts.  Also, Slipperymongoose has a laser tool and I have a Motion-Pro tool.  Not to hijack a thread or start anything, but here is more info if you want.  It's debatable on what tool is the best (laser, eye, Motion-Pro, or just counting the threads):  http://gstwins.com/gsboard/index.php?topic=61093

My brakes have a very slight rubbing noise (and I mean slight).  It may be normal.  My POS Mazda and Nissan have the same thing.

If you hear the rotor rubbing on the rear brake pads only at a certain position on the wheels rotation, I would think that meant a slight warp in the rotor more than a misalignment.

Chains will get tight and loose spots in them with age. This usually means that when you try to adjust it it will give a different readings depending on where the tight spots are. If this is the case you will need to replace it pretty soon.