The buzz is just about killing the note, standard .009 guages, the bridge is level to the body - it's not that hard to see if it's level or not.
OK, so it sounds like your close to your "perfect" setup.
There are several possible reasons your low-E is buzzing/fretting out.
The slot on the nut for the string is too deep/worn out?
You may need a little shim on the low-E side of the nut?
You may need a fret level and dress? If the second fret-wire is higher than the first, it's going to buzz.
You may want to try another set/brand of strings? I've had EXCELLENT results with Kurt Mangan strings.
You may have scarf joint shrinkage which will cause a slight back bow from the first to third frets.
You may want to raise your trem on the bass side a slight bit. Level (as viewed from the rear of the trem) is not necessary, playable is.
Did you shim the neck? if so do you have pics of how you did it??