Fret Level and Setup on Epiphone 339

This little semi acoustic guitar came in for a setup to get the action lower and to remove some unwanted buzz and dead spots. On first inspection I the nut was high and the radius of the strings at the bridge was all over the place so I thought a setup would cure the issues. However the I looked closer I found the frets were all over the place too so to get a good low action the only thing I could was level the frets. Now has a very very low action.