Go JIS. While I don't have a Filco, I do have a Cherry G80-3600 JIS model. Yes, it will be a nightmare to find replacement spacebars for Filco JIS as they don't use a friendly size. As far as the extra keys they do send a distinct scan code and can easily be remapped via software on the OS level with utilities capable of scan code reassign available for whatever OS.
Personally, I find JIS layout more intelligent that ISO. When using other than Japanese key maps, you get all the punctuation on the right side... not one random out of place punctuation key between left shift and 'z' where it makes no sense.
As far as hardware replacement controllers like bpiphany's... I don't see any reason why you couldn't use it if you wished, as the JIS TKL/Full keyboards share the same PCB revision as far as I know. The only 'problem' you should encounter there is having to adjust the keymap in the firmware. Only the plates are different to accommodate the extra keys.