What you are feeliing right now is perfectly natural. Most musicians get to that stage after a few years of regular playing and practing and I can assure you that you will feel like this again in the future. There is nothing wrong with that...it's a good thing. As frustrated as you may feel with your abilities and application right now you have identified weaknesses and want to resolve them so that you can move forward and improve your musicianship. That means you do not want to settle with what you know and can do. You should be encouraged by that.
To me, it sounds like you could be struggling with improv playing, which most people do after a few years of playing. A Phrase Trainer could be the ideal tool for you to practice, experiment and apply your music theory. You can use a Phrase Trainer to practice you runs, scales and modes, soloing and for general excercise. A couple of my students use them. You can plug in your CD player or MP3 player into it, filter out the bass and practice whatever you want to the music. Thats really good if you want to experiment with the current songs that you are playing and open up lots more runs that you could play. This exercise also helps a lot towards improv playing; ask your keys player to record a basic 2 or 3 chord progression with a steady 4:4 beat in several different keys (4-8 bars of one key then onto another and repeat in random order) and play along to it with a Phrase Trainer or through your stereo. Now you have to create your own groove and melody over it. Chords are quite simpyly selected notes from a scale all played together and its up to you which notes to play or if you want to add more. This is where you can have a lot of fun experimenting with scales and apply your modal theory. You can also change the groove with each change of key and have fun doing that. Not everything you will play will sound right, but you will understand how to link up notes and shapes that your scales produce and be sensitive to the pace of the music and the melody. There is lots you can do with this type of excericse, but improv playing is quite simply all about timing and spacing. This is the ideal time where you can construct and deconstruct your scales and create your own basslines, grooves and runs. Pretty soon you will find yourself naturally doing this as you are playing with your band. It is not an overnight thing...you will be constantly challenging yourself to do this for the rest of your playing life. There is a lot of discipline that you have aquire as you go along. Remember, the bass is a rhythm instrument that keeps the band together and you have to practice a lot of decorum to ensure that you don't overplay too much.
