No big deal,
you were just off in your calculations a touch. the 13/31 gives a ratio of 2.38, (31/13)= 2.38. With a 39 tooth it equals a even 3.00. Oh yea! Your screaming on the top end to get any speed. We figured at one time you loose roughly 1.10 mph for every tooth up on the axle sprocket. The only way I found to balance out the problem to an acceptable compromise is to use a 14/38 gear set in the trans. you'll get back approximately 3 mph without loosing any noticeable torque.
Another route is to tune the motor for the upper rpm range, IE: cam, head work, exhaust ,etc. The logic is since your forced to operate in the higher rpms because of the gearing, get the motor to function best up there. Tune the motor for higher end power and depend on gearing for the torque power.
There's so many frickin variables and strategies it's tough to figure what to do. Reminds me of a crap game!