Outside of any fitting problems, you need some conditioning for the new position to be comfortable.
The low "racing" position takes some time getting used to.

It's also possible that you are working harder than you need to to support yourself in the new position (ie, you might be tensing up more than you should). Where are your hands? It appears that most people mostly ride on the brake hoods. Moving from 10 miles to 35 miles is a fairly big jump.