My best advise would be to develop the systems separately (in different namespaces/machines whatever). Run unit tests on the new code (as we always should), and also compare the complete output of the both when ran over the same inputs to make sure that the results of the new are at least as good as the old (or why else would you make the new?).

When you are sure that the new system is complete and good, then replace the old system in its entirety.

To be more precise:

1. Make a copy of the old program and call it the new program.
2. Rewrite all of your classes/modules.
3. Test
4. Modify
5. Replace the old program with the new program.
6. Sit back and have a cigar knowing that you have done well.