Now that I have (almost) worked through the affix list and autohyphenated as many affixes as possible, I'm finding that editing the alphabetical files goes significantly more quickly. This is my editing procedure now:
-edit root entry
-autohyphenate all instances of that root in complex words in the file
-first pass: skim through all entries with that root and clean them up as best I can - mainly tagging any remaining morphemes and making sure gloss tags are placed properly in defs
-second pass: check that everything on the Lexware printout is present in the entries, and correct any autohyphing errors.
I could consider NOT even looking at the filecards from here on, to limit my obsessive need to proofread in triplicate. :-)