well I was going to suggest pro tools since you can draw in the wave form on low parts but I think that would be impossible to do with an already bounced down stereo track...it would more apply to a recorded bass track alone that was too low I think.

the parametric eq, mastering plug in ( I use ozone 3 but if you can get your hands on waves plugins go for it with those), and compressor ( raises up low sounds and lowers loud sounds to put it simply) will definitely help but as said above it's going to be a tough fix... mastering is hard enough when you have a clean mix to work with ( at least for me it is). notching with a parametric eq will help you hear what your doing much easier and quicker, then you will find the area to work on and lower/raise the notch till it sounds the way you want it (your also sweeping the notch horizontally from one end of the frequency spectrum to the other till you find the spot that pops out your bass in the mix). pretty much all these guys have given you sound "sound" advice. I recommend researching techniques and the theory of audio engineering as well, it will really help you not make this mistake again and be prepared if you do.

I used a compressor for a while without having a clue what it was really doing...actually I thought it was a limiter lol..then I went to school ( you dont have to go to school to learn about audio) and understood what it was actually doing, from there I taught myself or picked up various ways that a compressor can be completely awesome if used in variation with other effects such as delays and reverbs. it's like opening pandoras box but you can get a grip on it if you understand the theory behind it and then you can manipulate it into your sound.