The documentation on this ship is very sketchy, and it isn't a topic that I've studied in any detail. I'm pretty sure, though, that there is some contemporary evidence that the Bonhomme Richard was painted black overall.
Be warned: you're getting into extremely shaky territory here in terms of historical accuracy. Little is known for certain about the Bonhomme Richard. Many years ago the great historian of naval architecture Howard I. Chapelle wrote an article for the Nautical Research Journal called "The Ship Model That Should Not Be Built." His argument was that so little information is available about certain ships that modelers ought to avoid them. He put the Santa Maria and the Bonhomme Richard at the top of his list. Chapelle went on to argue that plenty of info about other famous and/or important ships IS available, and urged modelers to concentrate on them. Reliable contemporary plans of several other American ships from the Revolutionary War exist; it seems a shame that (at least to my knowledge) no manufacturer has ever based a kit on any of them.
The opposite viewpoint is represented by the great French researcher and draftsman Jean Boudriot. Some years ago he undertook to figure out what the Bonhomme Richard might have looked like, on the basis of extensive research in French archival sources. He published a book, John Paul Jones and the Bonhomme Richard, for which I personally have a great deal of respect. It contains a set of beautifully executed plans that reconstruct the ship about as well as anybody will ever be able to do. Boudriot would be the first to acknowledge that these plans are speculative, but few people would argue that they're wrong.
Some of the illustrations in Boudriot's book are by the American marine artist William Gilkerson. He got sufficiently interested in the project that he afterwards published a book of his own, The Ships of John Paul Jones. That one is also excellent. Both Boudriot and Gilkerson are fine sources for modelers.
I haven't seen the old Aurora kit for a very, very long time; I remember buying one about thirty years ago and giving up on it. I think what really turned me off was those awful injection-molded "sails," which were about six scale inches thick. It sounds like dscoggs has addressed that problem effectively. Given Aurora's reputation, and the state of the existing research at that time, I have an awful feeling that the kit in general is pretty thoroughly inaccurate. I never like to discourage people from such projects, the primary purpose of which ought to be to have fun. But I also think modelers deserve to go into those projects with their eyes open.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.