The structure may be complex with multiple load paths, but that's not true of the strain gauge. The strain gauge will only only measure strain in a single axis, and similarly that's exactly what you need to calibrate it for.
A good laboratory test rig will measure strain as a matter of course, so if you instrument up a testpiece with a strain gauge on it and a facsimile of your in-flight recording hardware you can come up with characteristics near-identical to what you'll have mounted in flight.
That'll give you discrete strain values in the gauge axes where they've been mounted. Translating that into stress clearly you need to know the cross section and material cross-section of the material it's mounted onto. If it's a complex structure, then you'll certainly need multiple gauges attached to it athough hopefully FEA (or just some competent back of envelope calculations) will indicate the critical bits to instrument.
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