We report on the impact of the preparation of the Si-face 4H-SiC(0001) Si substrate using a Ga flash-off process on the epitaxial growth of GaN by plasma-assisted molecular beam epitaxy. The nucleation, as well as the resultant structural and morphological properties of GaN grown directly on 4H-SiC(0001) Si are strongly influenced by the chemical and morphological modifications of the SiC surface induced by the Ga flash-off process. Herein we describe the impact of the specific concentration of Ga incident on the surface (quantified in terms of monolayer (ML) coverage): of 0.5 ML, 1ML and 2ML. The residual oxygen at the SiC surface, unintentional SiC nitridation and the formation of cubic GaN grains during the initial nucleation stage, are all reduced when a 2 ML Ga flash is used. All of the above factors result in structural improvement of the GaN epitaxial layers. The correlation between the SiC surface modification, the initial nucleation stage, and the GaN epitaxial layer structural quality has been articulated using x-ray photoelectron spectroscopy, xray diffraction, atomic force microscopy and spectroscopic ellipsometry data.