It's mostly a question of practice and having developed tools to help me transcribe; each strip gets typed into a custom OpenOffice spreadsheet (so I get fancy autocomplete etc. which I couldn't be bothered to write myself back in February when I made the first template), a macro turns that into XML and gets copied into the master file for each webcomic.
That gets mashed through a couple of custom PHP scripts to update the different database structures, then it all goes to a central update script to merge everything online. It sounds massively complex but the tools make the job pretty painless.
Generally the longest part is actually doing the typing, but for most strips, it's limited mostly to the dialogue and a few keypresses for each line (to confirm who said it and whether it's speech or thoughts or whatever)
I might actually make a blog post over on WordOwl in the next couple of days to demonstrate the actual process as it happens. It's really quick though, since most of the work is handled by code rather than me.
The recovery is going well, actually. I haven't lost anything massively significant and what I have lost may become found again yet, it's a question of sitting down with some other tools and gentle prodding, but right now I'm more interested in getting everything re-setup so I can use my PC again.