Mark,
I'd recommend avoiding digital zooms, they're always crud. They work by a process called 'interpolation", which to the lay man is basically guessing the missing data and making it up and adding it to the final zoomed image. You get all sorts of nasty artifacts as well with the image happening with digital zooms. Better to stick to optical zoom and crop imho. As Lester said, you needed more DOF, but at 48x...I don't think that there would have been much anyone could have done to be honest. I haven't played with focus stacking, so can't offer much advice. Best to read Brian's sticky and maybe ask him some questions about things that you're not sure on - he's the acknowledged master of focus stacking!
Dave