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Quadraped Z-Up Template fail

So Im trying to get the quadraped y up to work in z up project and a bunch of rotation channels are locked as Im trying to build a rig on top of an existing skeleton. When I try to rotate the guides im finding I have to unlock channels to get them translate and orient in right spot which Im not sure what problems this may cause.

Next is it generally safe practice to just orient the main parent guide 90 degrees to work in z-up for the template or will that rotation cause problems.

Does anyone have a quadraped zup template that isnt broken?? Please halp!!! and thanks in advance