As well as what fbates has said, the main answer is really - TIME - boring I know but you'll get there but start S L O W.... and work up. Keep going with concentrated exercises and you'll get there, there's no substitute for quality practice.
I have bought a Gripmaster which exercises individual fingers which is an amazing thing and has vastly improved my playing
and the 3 notes per string scales as you said has vastly helped but I have gone back to playing scales more with four fingers on each corresponding fret and going up and down as this method is usually prefered by bassists like Justin Raines as you can get more melodic runs out of it and it uses more economical playing with the left hand. S notes per string his nmore used by electric guitarists:
Finger exercises and finger stretching is very important EACH TIME before you play and will, over time, help you with your problem and loosen up your fingers:
Here's the 3 notes per scales explaination for those that don't know, but as I have said, this is more prefered by electric guitarists for legato playing:
Above all, DON'T ever get frustrated, it will come in time. The best thing I have learnt that improved my bass playing is using the pentatonic scales and learning slides and trills, this requires no stretching at all!
