While I can not give you a direct answer to your problem. I can tell you that there are other options out there that you should take a look at.

If you do want to work on the code yourself bioperl may be a good place to look. I myself have not worked with the tools there, but I get the sense others have done similar things to what you are trying to do. So there maybe something there that is helpful for you.

There are also numerous programs that grappled with Fitch's algorithm (and other algorithms for that matter), that might avoid the trouble of reinventing the wheel from scratch. For some helpful links to programs you might want to check out the Workshop on Molecular Evolution.

Sorry I can't help more than that.
Bio.