The auditory nuances of such a system are in the permutations of harmonics, not all of which can be modeled accurately without very serious resources. I don't want to discourage you. I like the idea of a hardware emulation using modern components but I think the result will not come without noticeable compromise in fidelity to the original.
The modularity you describe certainly will make it easier than otherwise. You should put the schematics up, if possible in PDF form.
In the meantime, here's some really good organ playing (classical):
https://www.youtube.com/watch?v=_pY08e_tdtA