Write , and . Since the background scalar has no spatial gradient,
Also . These are the linearized scalar-field matter projections; gradient energy first contributes quadratically.
There is a source convention defect in the shear formula. For the stated positive shift and spatial metric with , direct substitution into the extrinsic curvature gives the positive-shift scalar shear convention
There is no extra Laplacian in the definition of . Equivalently use : then the trace-free term has the printed minus sign and . This latter convention retains the printed momentum-constraint form. The source mixes these two choices.
At first order and . Combining their difference with gives
For the momentum constraint, differentiating the tensor above gives
For nonzero Fourier wavenumber, and absorbing the homogeneous integration mode into the background, the consistent momentum constraint is
Linearizing the scalar equation, the shift-advection term and lapse-gradient times scalar-gradient term vanish at this order because the background is spatially homogeneous. The remaining equation is
Insert , differentiate its lapse term, and use . The two background-acceleration terms combine into . Hence the perturbed Klein-Gordon equation with background lapse is
This scalar evolution equation and the Hamiltonian constraint agree with the displayed targets after the shear conventions are repaired.

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