What size counter shaft sprocket? 19 tooth? 20 tooth? 21 tooth?
With a 19 tooth, 6000 rpm should yield about 92 mph while a 20 tooth ups that to 97 mph, and a 21 tooth 102 mph. Of course that is with the standard 4.10-19 rear tire and no clutch slip.
That would be close to your observed 50 mph at 3000 rpm.