This project formulates a noncommutative geometric framework in which Standard Model fermion mass ratios, flavor mixing parameters, gauge couplings, and cosmological constants emerge as spectral invariants of a compact Riemannian 3-manifold $\mathcal{M}$ with degenerate double-helical (leptons) and triple-strand braid (quarks) topology. The vacuum geometry is constructed as a vertically oriented torus $\mathcal{T}^2$ with catenoidal minimal surfaces $\mathcal{B}_{\pm}$ connecting asymptotically flat sheets; its pitch and transverse scale are rigidly fixed by Pogorelov-type embedding constraints derived from the Euclidean metric signature $\{\sqrt{1},\sqrt{2},\sqrt{3}\}$. Starting from the real spectral triple $(\mathcal{A},\mathcal{H},\not D,J)$, the leading eigenvalues of the helical Dirac operator $\not D_{\mathcal{H}_{\rm elix}}$ are computed in the adiabatic approximation, deriving the mass scaling $m_f \propto |w_f|/R_{\rm eff}$ where $w_f \in \mathbb{Z}$ is the topological winding number. The continuous geometric prediction for the muon-to-electron mass ratio, $m_\mu/m_e = 2\Lambda_1^2(1+\alpha/2\pi) \approx 204.06$, matches experiment at the $1.31\%$ level without free parameters. The framework demonstrates that this residual deviation arises from topological frustration: the incompatibility between the continuous geometric invariant $\Lambda_1^2 \approx 101.91$ and the requirement of integer winding numbers for physical fermionic eigenmodes. Applying the Călugăreanu-White theorem $Lk = Tw + Wr$, it is shown that the system resolves this tension by deforming the helical axis. This geometric writhe $Wr$ acts as a kinematic spectral-flow penalty ($\mathcal{D}_k$) that strictly stretches the metric tensor of the vacuum, rather than acting as a simple additive phase. By integrating this metric stretching in quadrature with the two-loop vacuum polarization QED correction, matching to experiment fixes the physical twist number $Tw = 103$, yielding $m_\mu/m_e = 206.7683$ in agreement with data at the $0.1$ ppm ($10^{-7}$) level. Furthermore, the inverse fine-structure constant is derived as $\alpha^{-1} = \Lambda_1^2 + Tw/3 + \Lambda_3/6 + |Wr|/30 \approx 137.0370$ from discrete angular holonomy of the helical lattice with $\pi/3$ and $\pi/6$ torsional steps (Wilson phases on a triangular lattice), accurate to $0.0008\%$ (8 ppm). The Cabibbo angle emerges as $\sin\theta_C = \Lambda_3/(2\Lambda_1) \approx 0.2246$, matching experiment at $0.17\%$. New results: The framework is extended to include triple-strand braid topology for quarks, deriving the strong coupling constant $\alpha_s(M_Z) \approx 0.113$ (95% accuracy), proton-to-electron mass ratio $m_p/m_e \approx 1836.1526$ (8-digit accuracy via braid packing factor $\Phi_{\rm braid} = \sqrt{1 + \Lambda_3/N_{\rm twist}^2}$), and baryon asymmetry $\eta \sim 10^{-10}$ from chiral braid asymmetry. The project predicts the complete CKM matrix: $\sin\theta_{12} = \Lambda_3/(2\Lambda_1)$, $\sin\theta_{23} = 4\Lambda_1^{-1}\sqrt{|Wr|/N_{\rm twist}}$, $\sin\theta_{13} = \Lambda_3/(12\Lambda_1^2)$, and CP-violating phase $\delta_{CP} = \arctan(\Lambda_1/\Lambda_3) \approx 65.8^\circ$, all matching experiment at sub-percent precision. Cosmological predictions include dark energy $\Omega_\Lambda \approx 0.685$, spectral index $n_s \approx 0.932$, reheating temperature $T_{rh} \approx 3\times 10^{10}$ GeV, and inflationary expansion factor $\sim 10^{14}$—all from pure geometry with radically reduced phenomenological dependence. The framework predicts a falsifiable Planck-scale Lorentz invariance violation: anisotropic muon decay with amplitude $\eta = (2\pi)^{-1}(r/R_t)(\alpha/\pi)(\Lambda_3/\sqrt{Tw}) \approx 1.18\times 10^{-4}$, testable in polarized beam experiments. Explicit error analysis is provided, the domain of validity of approximations is discussed, and the full Flamewalker Protocol (FWHP) epistemic audit architecture (Streams A-C v3) is documented, demonstrating that the geometry survives hostile null-model destruction, Westfall-Young FWER control, and first-principles heat-kernel derivation of vacuum decoherence with $\xi_{\rm theo} = 0.03427$ (deviation $4.81\% < 5.0\%$ tolerance). All results are strictly separated into Layer I (empirical), Layer II (formal/topological), and Layer III (interpretative) per FWHP discipline.