After a week of struggle, correctly identifying crufted permissions applied in layers dating back to around 2000, when I first installed OS X on the home server, I concluded that a drive wipe and clean reinstall was the only way to sort things out.
This has proved partly true, in that permissions have been the cause of my pain and suffering, and partly untrue, in that the frustrations I have been experiencing with them can now be definitively attributed to the Mac OS X default user structure.
I am quite close to a resolution, however. I have been able to connect to my crufty MySQL databases via PHP. Perl is still complaining, but does appear to be trying to talk to the databases.
With luck, tomorrow, I can extract the data needed and start shifting miscellaneous stuff over to the hosted environment.