While I had the rear shock off the bike, I decided to confirm some chain adjustment numbers.

With the shock disconnected, it is easy to raise and lower the rear wheel and my goal was to align the rear wheel so that the centers of the front sprocket, swingarm pivot bolt, and the rear axle were in a straight line. This alignment of the wheel gives the longest distance between the sprocket center and the rear axle center, and the chain will be at it's tightest in this position.

I put small diameter pins into the swingarm pivot bolt and rear axle for a ruler to rest on. I could then raise and lower the wheel and see where the ruler was in relation to the front sprocket.

<-- In this picture, the rear wheel has been raised so that the centers of the front sprocket, swingarm pivot bolt, and the rear axle are in a straight line. The ruler is slightly ABOVE the imaginery line through the centers. Note that the ruler is also slightly above the transmission drive shaft center that the front sprocket is mounted on, just about where it would be if it was resting on a pin that was inserted into the end of the shaft. (The shaft is not hollow, so I could not put a pin in it.)

With the wheel in this position, I adjusted the chain adjusting bolts so the chain had about 1/2" of slack, measured midway between the swingarm pivot bolt and rear axle.

<-- In this picture, the rear shock is installed and the spacers under the rear wheel have been removed and the wheel is off of the ground. The shock is extended to it's fullest. The pins and ruler are in the same position as before. Note that the ruler is higher than before where it passes over the sprocket, but not by much.

The higher front on the ruler means that the rear axle is lower than in the aligned position. The very small amount that the rear axle is below the alignment line is not usually seen in a 'dirt' bike (trail bike, MX bike etc). Usually, the rear axle is much lower and the swingarm tilts down considerably towards the rear. Further, when the WRR is taken off the stand and lowered to the ground, the swingarm will swing up to level or past it as the bike's weight compresses the rear shock slightly. When I get on the bike, the swingarm will definitely be past level and probably angled upwards in the rear.

The reason for this peculiar geometry is that I have installed a YamaLink in place of the stock Yamaha shock link and I have lowered the seat height by screwing the shock clevis in so the shock is shorter overall. These two mods have substantially altered the stock rear shock and swingarm geometry. The question is: Is this bad? My experience is that this is not bad ON THIS BIKE. It would be very bad for an MX bike, but for my WRR, which is ridden primarily on dirt roads and some easy trails, it's not bad at all.

One other consideration: I had the rear shock revalved by Go-Race and I told them about the suspension modifications I had made. I suspect the shock has valving that is adequate for the peculiar geometry. What am I saying? I know it's adequate because my WRR rides just fine with the mods and shock revalving! I couldn't be happier with how the suspension performs.

Now back to the chain adjustment numbers I was looking for when I started all this.

<-- The left picture shows the chain height above the swingarm when the bike is on a bike stand and the shock is fully extended. The number is 38mm.

The right picture shows the chain height above the swingarm when the bike is sitting on the ground with the side stand down and the shock slightly compressed by the bike's weight. The number is 37mm. -->

These numbers bear no relationship to the numbers in the Yamaha Owner's Manual, Service Manual, or Technical Bulletin M2008-20. All of Yamaha's numbers are measured below the swingarm whereas I prefer to measure above the swingarm so I don't have to stoop so low to see the ruler.

My measurement is the distance between the bottom of the chain and the top of the swingarm protector with the chain pulled up away from the swingarm. My measurement is taken at what I judge to be the point at which the chain lifts the farthest from the swingarm, about half way between the front and rear sprocket centers. This point is about 1" forward of the back end of the swingarm protector.

Note: a larger measured distance indicates a looser chain.

<-- The left picture shows the chain distance below the swingarm when the bike is on a bike stand and the shock is fully extended. The number is 19mm.

The right picture shows the chain distance below the swingarm when the bike is sitting on the ground with the side stand down and the shock slightly compressed by the bike's weight. The number is 20mm. -->

My measurement is the distance between the bottom of the swingarm and the top of the chain with the chain pushed up towards the swingarm. My measurement is taken at what I judge to be the point at which the chain is closest to the swingarm, about half way between the front and rear sprocket centers. This point is about 13" from the front sprocket center.

Yamaha measures with the bike on its side stand so the left number is not relevant; the bike is on a stand. The right number is measured with the bike on its side stand and at about the same place Yamaha measures. My value of 20mm differs from Yamaha's 8-13mm because of three reasons: I like my chain tighter than Yamaha recommends, the suspension geometry has been changed by the YamaLink, the chain/sprocket geometry has been changed because I use substantially different sprocket sizes than stock (12/47 vs 13/43).

Note: a smaller measured distance indicates a looser chain.
 

Note that these numbers apply to my WR250R with the following changes that relate to bike geometry:
Front sprocket 12T
Rear Sprocket 47T
Drive chain 110 links
Shock clevis screwed in as far as possible (lowest seat height)
YamaLink lowering link installed
Fork triple clamps lowered
DOT trials tires fitted front and rear

And now, a word about measuring chain slack/play/free play/clearance/tension. Yes, there really are that many terms for slack. I know, I looked it up on the interweb. There are undoubtedly other words as well, but I had to stop somewhere. And not only are there many words for the measurement, there are many ways to perform the measurement. Most of the ones I found measure above the swingarm, but they measure either static maximum distance or up and down play using different reference points (chain link center line vs top or bottom of chain link). Here is the most concise statement I found: "Slack is how much the chain will move up and down freely at a point halfway between the two sprockets."

I prefer 'above the swingarm' and static maximum height as noted previously. For each new bike, I perform the foregoing measurement procedure to get the bike's precise chain slack measurement. It's a bother, but I have confidence that I determine and use the correct chain slack measurement. However, I think Yamaha's method for the WRR is a pretty good way to do it also. YMMV