Chain adjustment and rear wheel alignment

[Nath]

I done a search for chain adjusting and rear wheel alignment but most of the ones I found related to the S2 and not the 2004-2006 FZ6s and the have very different swing arms.

I read this http://www.manualslib.com/manual/805140/Yamaha-Fz6-Ss.html?page=125#manual and decided that mine at 35mm was too tight. 

I undone the axle nut and loosened off the chain and adjusted it to 50mm. Am I correct in stating this is done by measuring it at it's highest point to it's lowest point at the tight spot?

When I set it to that and done up the lock nut the right side of the wheel (brake side) was showing some thread and the nuts weren't snug to the arm. I undone the axle nut again and pushed the wheel to what seemed more accurate and done it up and that levelled it off. Does that often happen?

I measured the distance from the axle nut washer to the end of the arm and both were pretty much spot on. I then measured with a digital caliper the distance from the arm to the end of the adjuster and they were both much the same as well.

After all that waffle is measuring the distance from the end of the arm to the end of the adjuster bolt an accurate way to do it? I wasn't sure I was over thinking the simplest of things of just adjusting a chain and re aligning the rear wheel.

[chaz]

I aim for 50mm slack this is the amount you can move the chain up and down without putting any force on it, I measure the amount of thread on the adjusters to aline the wheel, I have checked that they are the same length, when I had the wheel out, seems to work ok.

[Nath]

Cheers Chaz for your reply