this is the course that my training took, i.e. began with aikido and eventually shifted into Shinto Muso-ryu jo. i think the advantage with starting out as a student of a gendai school and then moving into a koryu group is that, in general, gendai schools will give you a good grounding in the traditional behaviours and etiquette without expecting you to understand those things right from the jump. naturally, every school has their own character or atmosphere which must be "internalized" or "sussed out", but there are baselines that are almost always respected.
the language issue is perhaps not as big a problem as you might imagine, but i can't discount the usefulness of strong japanese skills. having one ear open and ready to take instruction shouted from across the dojo floor helps to avoid teacher frustration! the upside is that most koryu teachers expect you to speak even less than gendai teachers do: shut up, follow their instruction closely, and most times everything should go smoothly.
i don't think that there are too many "bad habits" that one can pick up from gendai training. only if you persist in trying to maintain a habit that your new koryu teacher has told you to give up will you run into trouble. as my jo teacher often says, "strive to avoid having me repeat an instruction; if you fail to correct yourself, then the meaning of training is lost."
unlike other heavyweights here, i don't speak from a wealth of experience, but i believe that what i've written is true of my own experience with koryu training. if you have any other questions, please don't hesitate to write again. if you haven't had a chance to check out some of the articles at Koryu Books about getting a start in koryu arts, i'd highly recommend them.
Jeff Hamacher
Those who speak do not know,
Those who know will not speak ...
So I guess that means I don't know a thing!