Velocity is a vector, it can have any directions. It is speed, the magnitude of velocity, that can not be negative.
You are right, the force is considered positive with respect to the acceleration if it has the same direction as that of the acceleration.
Now, about normal force: The (centripetal) acceleration points toward the centre. If the bead is at the top of the circle, gravity G=mg points also towards the centre so it is positive. The centripetal force is the sum of gravity G and the normal force R1. All these forces are vectors, they act along the vertical direction now. You found that R1=mv2/a-mgcos(theta). Calculate, R1 for theta =0, 30° and 40°, please, and tell me what you got.
ehild