I wrote up the procedure I use to create 3D Google Earth plots based on a thread found here on TRF. Unfortunately I don't have a link to that thread, so my sincere apologies to the original authors that contributed their efforts.
One thing that is common with nearly all the rocket GPS trackers I have used is missing data during assent, especially on higher performance flights. Mounting can of course also affect the quality of the data received from the GPS satellites which affects data smoothness.
I hope this helps,
Tony
Convert Featherweight tracker data to KML files.PDF: