Precise measurements of the proton electromagnetic form factor ratio $R = mu_p G_E^p/G_M^p$ using the polarization transfer method at Jefferson Lab have revolutionized the understanding of nucleon structure by revealing the strong decrease of $R$ with momentum transfer $Q^2$ for $Q^2 gtrsim 1$ GeV$^2$, in strong disagreement with previous extractions of $R$ from cross section measurements. In particular, the polarization transfer results have exposed the limits of applicability of the one-photon-exchange approximation and highlighted the role of quark orbital angular momentum in the nucleon structure. The GEp-II experiment in Jefferson Labs Hall A measured $R$ at four $Q^2$ values in the range 3.5 GeV$^2 le Q^2 le 5.6$ GeV$^2$. A possible discrepancy between the originally published GEp-II results and more recent measurements at higher $Q^2$ motivated a new analysis of the GEp-II data. This article presents the final results of the GEp-II experiment, including details of the new analysis, an expanded description of the apparatus and an overview of theoretical progress since the original publication. The key result of the final analysis is a systematic increase in the results for $R$, improving the consistency of the polarization transfer data in the high-$Q^2$ region. This increase is the result of an improved selection of elastic events which largely removes the systematic effect of the inelastic contamination, underestimated by the original analysis.
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