If your 3rd position and mine are the same you are playing D Major and A Major scales?
Ideal for reviewing the three basics of shifting - Position to Position (2 different settings of your hand, like notches on the neck) - Distance between Positions (measured by sliding thumb up/down the back of neck and 1st finger up/down the string) - Prehearing the note you are about to play.
Also ideal for reviewing your shifting technique. This may be hindering your moving cleanly to the next position.
Practice the D scale descending - 4 2 4 1 0 4 1 0. Tune the top D carefully to the D harmonic above it and check against the open D string. Play down the scale slowly and deliberately in two groups of four notes, pausing briefly between groups. Try to pre-hear the notes coming. Then try going up the scale. Feel the distance travelled and feel the arm and hand settings at each end. Each group (going up the scale) has the same structure, Tone Tone 1/2 Tone, with a Tone between the groups.
Matthew is right - we are training muscle memory. We are also using our ears to train our muscles.
Try this note-finding muscle-memory trick. Locate the top D carefully with your pinkie then shut your eyes and think about how the settings of your left hand and arm feel. Take your hand away, look at the ceiling and put your hand back where it just was then test with the bow. Adjust, think about it again, scratch the back of your head and try again. Repeat, scratching somewhere else or touching the top of the scroll. Within a few goes your hand will start landing so close to D that corrections are small, fast and easy. Then find A, the 5th above Open D string, with your 1st finger. Repeat the above processes until you can do them successfully at least three times in a row every time you pick up the bass.
Now shift back and forwards between A and D, glissing if you want to, prehearing the note coming, feeling the distance travelled with your "tape measure", and feeling the settings at each end of the shift.
After a lot of teaching I have simplified learning into a 3 letter acronym, "HEE", short for Hands Eyes and Ears. Your eyes read the notes, your hands make the notes, and your ears guide and train your hands and are your quality control. So much of successfully playing the bass is about your hands, their use, shapes and movements. Your left hand is the Technician, finding and linking together set places on the fingerboard. Your right hand is the Magician, holding your magic wand (the bow) and sounding and connecting the notes into beautiful lines. Each has very different jobs to do yet they have to work very closely together. This is where good shifting technique comes in.
Happy hunting!!
DP