Sorry if I came accross too preachy, but it is good to know how to play in every key.
I was going to suggest transposing in Cakewalk, but I'm not sure if that would get rid of the harmonizing problem. It's worth a try, however.
There is a program, I think at SVPworld.com where you can create a midi sequence in Cakewalk and hang onto the sysex information containing the chord changes that you need for harmonizing.
Larry