Hi, Bran.
Unfortunately, the "Tironian et" wasn't included in even the largest Adobe Latin 5 character set*, so there probably won't be a glyph name assigned anytime soon. But that's not a difficulty. Skip the little green gem routine and manually enter as a glyph name "uni204A" and "204A" as the Unicode index info (both without quotes, of course). Type in that "uni" as lowercase and that "A" as uppercase and you should be good to go.
Perhaps someone else can address the "glyph positioning rule exceptions" you mentioned. I don't see it as a related issue
if the glyph naming is correct.**
Hope this helps. Good luck.
* Should you be interested, extensive notes about Adobe's extended Latin character sets can be found at
http://blogs.adobe.com/typblography/2008/08/extended_latin.html** If you still have troubles after renaming the "et" as above, try this simple test: Create a new, blank font and open, say, the uppercase "A" slot. Whether you draw a dot in there or nothing at all is immaterial at this point. Try to reassign the glyph name and Unicode index as above using the "Properties" panel (on Win, use a right mouse click for the flyout menu or Alt+Enter; for a Mac, um... sorry, but I forget). If that works out without a hitch, perhaps you have problems elsewhere (e.g., a .vfb that's gone screwy).