A 120 link chain will have to be cut down for any of the combinations you mention. For example, I run 112 links with 13/51 sprockets on my WR250R. Some riders aren't confident in selecting the specific chain length they'll need so they order the longest available for the same price and just cut it down.
With stock gearing the speedometer reads about 7% higher than actual speed. (This is apparently intentional by Yamaha.) The speedometer sensor is in the gearbox, so any sprocket combinations resulting in higher gearing than stock will increase the speedometer error. Tire choices with different circumference than stock tires will also affect speedometer accuracy. All can be corrected with a speedo healer.