I don't know much about this old stuff, but I'd probably use Unicode slots for those special characters...
For modifying fonts that don't have them or have them in various other slots (and it's probably why you see them marked as "?") you could try TypeTool 3 on Windows or FontForge on Linux, although FontForge can also run on Windows... The cleanest way would probably be running a LiveCD Linux distribution (eg. Ubuntu) using VirtualBox and just install it from the included Synaptic package manager. But it can also be done with Cygwin (if you don't mind some 35.000 files install). I ran it back in 2009 or so (see the screenshots):
http://www.diybookscanner.org/forum/....php?f=3&t=194