The historical logs have a time stamp associated with each data point. If I remember correctly, I pulled each log into excel as a .csv file and then deleted every line with a speed < 15 and every line with an invalid GPS coordinate. The result was (hopefully) taxi/takeoff roll to landing/rollout. For flight time, I subtracted the first data point from the last. It's laborious to do manually, but a script can do it in a few seconds.
It goes without saying that a valid GPS fix is required for this to work. It also seems like quick reboots in flight would continue the same log, but a brief delay between sessions started a new log. In those cases, I just appended the log files together.
Also, I think iFly has hinted that a logbook feature is somewhere in the pipeline.