A few thoughts:
Are there already matching screwholes in the body and neck? If so, does screwing together the body and neck put the neck in correct alignment i.e. where it needs to be so the bass can be usable?
If there aren't any screwholes (or the existing ones don't line-up) then you will (obviously, sorry if this teaching you to suck eggs) have to position the neck in alignment, drill new holes and put in screws. You could maybe use some spacers on each side of the neck to hold it whilst you check the alignment. It could be that the pocket is not cut centrally and there iwill be a slightly uneven gap on each side of the neck.
When you are happy with the fit of the neck then you could maybe fill any gaps with wood. I'd do one side of the pocket at a time: neck off, cut wood to correct depth and length but leave slightly wide. Put wood in place ('dry fitted'), put neck in place (wedge the gap on the other side to hold neck snug against the wood) and test for position by seeing if you can place the screws in. Reduce thickness of the wood a small amount at a time until the screws fit in.
Once the neck fits, remove the wood from the first side and repeat to fit the wood on the opposite side. When you are happy with these filling pieces and the fit of the neck, then glue them in place and do any finishing or paint touch-up etc.
Let us know how you get on.