I don't think there is a 64Kb limit for code, there certainly is for the current leJOS garbage collector (but this is due to design decisions in the software rather than any hardware issues). You are correct in that the sizes set in the firmware basically just tell it how much space has been used by the firmware and the menu system and hence how much space is available for the file system.
Good luck with the project, let us know how you get on....
Oh and are there any papers etc. that describe Keiko? A quick search turned up...http://spivey.oriel.ox.ac.uk/corner/Des ... ts_for_OBC
(I assume the corner is yours!) andhttp://peterdn.com/files/A_JIT_Translat ... Oberon.pdf
Is there anything else?
It's a long time since I looked at Oberon and Niklaus Wirth. It took me back a bit. I spent a lot of time playing/working with Pascal-S and the Pascal P compiler along with Solo and the original version of Modula in my undergraduate years, interesting to see how things have developed...
All the best