On average, how much does it cost to adjust all the frets on a bass's neck?

Frets are not adjusted per say. A fret leveling includes filing the frets level and then re-shaping them. It is a pretty big job.

 

No, because a new Mex Fender nick might need the exact same process carried out.

I bought one of those brand new Fender Mex Jazz necks a couple of years ago. This was during the period Fender offered bodies and necks for sale as stand-alone items. The neck was not player ready. The nut needed to be filed correctly, the frets needed leveled, crowned and polished, and the board needed scraped and oiled. I also needed to install tuners and a string tree, and the hole for the tree wasn't pre-drilled.

 

That could be the case, but I would suspect that the neck has a back bow and that the truss rod needs an adjustment. The nut being too low would only really affect open strings. Once you press down at the first fret, the nut isn't really part of the equation anymore.

 

Sounds like the neck needs some relief, try loosening the trussrod a little.