When replicating results, what should I do when the author didn't use the method the paper said they did?
Given that you don't have space enough to present all three sets of results, I would suggest that you choose the parameters that best illustrate the scientific point that you are aiming to make.

When you state the parameters, however, you should add a parenthetical note or footnote that says something along the lines of:


  Note that we have chosen these parameters because [REASON].  Alternative parameters given [in the original paper / by the author] produce results that are [better / worse].


This balances the openness of making sure the reader is aware of the choice you have made and its consequences, while at the same time restricting your presentation space budget to only the most relevant set of results.