I usually just sand a bit off the bottom (or shim it up). You really need nut files to lower the grooves properly (although there other methods for that)

Fit it without glue and let the string pressure hold it in place and just slowly take a bit off the bottom by gently sanding on a flat surface with 180 grit until you are happy. If you have vernier callipers you can measure the e string slots to verify you are taking off the material evenly