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question about referencing code...

Treat code the same as any other bit of work, treat your work like your writing a publication because if it's any good that's where it will end up.

Your code is (or at least part of) your 'methods'. Did the person make a significant intellectual contribution to your method? If so, then they go on the author list. Did they help out just a little? If so, they go in the acknowledgements. Of course there are other factors such as politics and regional/lab/cultural issues when dealing with author lists to consider as well. Obviously this is just my personal opinion.

will bad data / methodological issues fail my thesis?

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I had pretty much the same experience with my first chapter. I conducted an experiment, the treatment failed but I noticed an interesting result not covered by the original aims. I was given the same advice as you, write it up with the new result as the main objective. This may not make sense to you, but that is not the point. The point is that you found a result that is statistically valid and theoretically sound, your job is now to communicate that result. Basically the original objective / hypothesis confuses the reader.

But I'm sure other people may have different opinions on this, anyone care to comment ....