To be honest I have no idea on the data formats they are stored in or how easy it is to export them. I tried to quick-scan the source codes for hints, but I can't find them. Then again, I believe database query code doesn't usually show up in the source code anyways (at least if it's written in php, it shouldn't in php, right?) In any case, I guess it's likely that the format will be similar to the Mandarin database, right? Anyways, the web pages are:Do you have links to the data in a usable format and some general information? I don't really know anything about Minnan or Hakka.
Considering the stuff you got converted already, you might well succeed where I fail
The page for the 台日大辭典 is http://taigi.fhl.net/dict/ although sadly only a translated version (into Taiwanese Minnan) can be searched. You do get a link to a scan of the corresponding original page with every entry though.