This looks the most promising, and has the ability to preserve the 'known' events (marked correct for this reason). I also like the ability to use this in flight as the rocket may one day have a reason to know its flight properties in flight.

Thanks a lot for the linked papers. I'll have a good amount of reading to do this weekend.

Also, thanks for the wiki link, I didn't find that in my search.

I actually did this before ever asking the question, and the numbers were a little choppy, so I wrote a program which repeatedly does this until the numbers smooth out enough to get decent data, but it also caused the curve to flatten at the top and bottom of the flight, so I think my values are off a bit from the real answers. Is there some kind of normalization that can be run after averaging the values to bring the curve back to its original height?

How not? I am asking for suggestions on a numerical analysis question, not for someone to hand me a transformed data set... I didn't even include the full data set in the question, it was just added to show people the noise the question is dealing with.

Down vote without explanation?