Three strategies for evening out an uneven bass guitar
What to do if there are uneven notes in the bass?
The first thing to try of course is compression, if you're not already compressing it — that can help! I tend to start with an 1176-type compressor with the attack and release set all the way fast (7, if it's a skeuomorphically accurate 1176 knob that goes from 1 to 7). I start with a 4:1 ratio, although other ratios can be good too depending on the song. Then I adjust the input / output / threshold until it levels out some.
If it's more that individual bass notes here and there are too loud or too soft, you can just go into the waveform and separate out the notes and turn their clip gain (waveform size) up or down. I do this a lot.
If it's more that certain notes are too loud or too soft every time that note is played — for example, every low E is too loud, or every C is too quiet — like maybe some unevenness in the frets or whatever — then I tend to deal with that with very precise EQ points, one per note. For example, if the C is too quiet, then I will look in a note-to-frequency chart (google it if you need one), learn that the C in question is 131 Hz, and then I will make a little eq poke something like this: 131 Hz, Q=10, +4 dB. Adjust the Q and gain of the eq until the note sounds smoother in context; sometimes a wider Q will sound more natural. It depends what's happening around it and what else is happening in the part harmonically. You'll be able to hear when a boost sounds like it fills in the hole perfectly (or neutralizes a boomy note); sometimes a more surgical approach is better (Q=8 to 10) and sometimes a less surgical boost works better (Q=4 to 8).
Boom boom — jamie