"Mine was .25" at the rear ISO and .31" at the front resulting in a skewed power train, swing arm & wheel."
Re: your quote above, the ISO shims on the left front & right rear as you describe not being equal could skew the drive train but you will only know if you determine what are the specs on the shims on the other side (of the frount & rear). In theory the ISO should have the same shim thickness on ether side of the frount & on the rear ISO.
I know when I rebuilt my ISO's to obtain the correct clearence I ended up with slightly different thickness on one side on both frount & rear. I put the greatest thickness on the sides I couldn't latter easily reshim (the front right & rear left) in anticipation of it needing additional shimming latter & the extra shims being on the opposite side will be actually be improving alignment of the drive train. After break-in I did have to add 15 thou to the rear ISO (right side)...
Having said all this the recomended way to check the wheel aligment is using two straight edges against the front & rear tires. I havn't had to try this however as my commando handles great as is.