16.09 RC1 has AutoTune. You might give that a try. AutoTune tunes the non-GPS modes (which are automatically used by the GPS modes too).
Read at least the important part of the AutoTune wiki for that.
The simple version is:
- use stock PIDs (or known, slow, smooth PIDs) in bank #1
- set up FMS (flight mode switch) for
--- FMS#1 Attitude mode manual throttle (Stabilized 1) on bank 1
--- FMS#2 AutoTune mode on bank 1
--- FMS#3 Attitude mode manual throttle (Stabilized 1) on bank 3
- take off with FMS #1
- switch to FMS #2 and after 2 seconds, it will shake around for 60 seconds
- land after shaking stops
- disarm
- switch to FMS #3
- arm
- carefully take off to test the new PIDs (be ready to instantly drop by using zero throttle if anything strange happens)
If everything works, set up FMS as you like, with all modes pointing to bank 3