wxp - you only allowed 48 hours - and on a holiday weekend at that - for folks to leave comments. While many of us frequent this site quite a bit, we do have other things in our lives, too!
This topic has also been discussed in other threads before, so one must be patient when asking for help, and also diligent about searching for older threads on related topic, though I can also see that our search function isn't working very well right now.
As to swingarm alignment, if things are working well before you first took the swingarm off, the thing is to measure the gap between the swingarm and the frame bosses at the pivots on BOTH sides, and restore the swingarm to this gap or as nearly close to it as possible when reinstalling. While it is fairly important to get the swingarm more or less centered in the frame, it is more important that you don't have any rubbing of the drive train inside the swingarm tube on the right side. Ideally one would have it so that the driveline is exactly centered in the tube, but this isn't always easy to do (or see, for that matter), so most of us rely on checking the gaps between the frame and swingarm at the pivots on both sides as mentioned before.
It help to take pictures (especially if you have a digital camera) as you go so that you know ho it all goes back together, and to help document your observations & measurements. I'd recommend using calipers for a more precise measurement than this tape measure, but this at least gives you the idea of what to check. Do the same thing on the other side. If the bearings are all properly installed and preloaded and the frame isn't tweaked, this measurement should be pretty close to the same on each side, but it won't necessarily be exactly the same for the driveline to be exactly centered in the tube. Again, once I find where it seems to work well on any of my bikes - or I see that it has been OK on a "new" bike, I tend to always restore it to the same spot.
If you do have the small 12-point, closed-end wrench that comes in the toolkit and no torque wrench to fit the bolts, then it is probably OK to use the "goodentite" method for torquing these bolts. There is an often controversial debate as to whether these bolts can be re-used or not - I generally use new bolts every time, and keep a few old/used ones as "spares". These bolts either come with a locking washer or some do not (stretch bolts). The stretch bolts are recommended by BMW to not be re-used, and I tend to follow this part of their advice, though I know others have re-used them without causing global economic meltdown.... hey, wait a minute !
1) make sure the rear brake is hooked up and have someone really push hard on the brake pedal to stop the rear wheel from turning.
2) make sure that wrench is fully engaged and squarely on the bolt head to be tightened and give it a good hard tug. Unless you're stronger than the governor of Kalifornia you won't be able to overtorque those bolts with that little wrench, and you will probably be able to get them tight enough for practical purposes unless you're a real wimp.
Do read, and re-read "snowbums" web pages - he is very verbose and often goes off on a tangent (and his web page organization is atrocious) but there are alot of good "gems" in there for maintaining airheads. Bookmark his site and re-visit it from time to time, and of course, feel welcome to join us here to discuss things, too!
Mike
