If I'm -sure- the frame and swingarm are both straight, I simply measure from center of the rear axel to center of the swingarm bolt. When both sides are equal, the wheels -should- be aligned.
This method works well, providing nothing is bent or badly worn.
On an unknown bike, I use the 'two straightedge' or string method when checking alignment for the first time, then check and note the C to C axel/swingarm measurement for future reference.
Here's a nice description the string method: (disregard the "y word")
http://www.yamahafz1oa.com/sportryde...ntmethod.shtml
The straightedge method is the same routine, using two 8' long perfectly straight pieces of most anything in place of the string.
Chain play on centerstand will vary a bit according to rider weight and shocks. Try 1 1/2"-1 3/4" to start, then check under load and adjust accordingly.
You'll need a helper. A nubile redhead is my personal favorite.
