Changing an experiment due to preliminary data I'm writing a paper comparing the performance of 2 algorithms (lets call them A and B). A performs better than B, however preliminary data suggested a way to significantly improve the performance of B. I made the changes to B and sure enough now B outperforms A. I've verified that it's not just a fluke of the specific inputs I was testing against, making the changes to B leads to consistently better performance. 

What is the best way to write these findings up? It feels an awful lot like cherry picking to me (especially since I didn't know when I started that I could improve B and for all I know there are improvements to A that could make it better than the improved B) 

But despite its questionable origins the modified algorithm does perform the task faster and I want to include that information in my paper.

What is the best approach to take?
Call the modified version Algorithm C and just add it to the paper?
Add this information to the appendix?
Something else?
Consider this:
What question is your paper trying to answer?

This is the real question to consider. If I were writing a paper about average milk production of cows and my question was "How much milk does the average cow produce in a year?" and then I only selected the 10 best cows, then I am really answering the question "How much milk do the 10 best cows in my selection produce in a year?".

If your paper's aim is to compare two or three algorithms, then there's no problem. If you write a paper about A and B, it's no different from writing a paper about A and C or A, B, and C. How you arrived at the algorithms does not change question you are answering.