This is the subsequent paper to our recently published rapid communication eporting new results from a study investigating the role of substrate temperature in the deposition of diamond films using our newly developed time-modulated chemical vapor deposition (TMCVD) process. TMCVD was used to deposit polycrystalline diamond coatings onto silicon substrates using hot-filament CVD system. In this investigation, we have studied the effect of (i) substrate temperature and (ii) methane (CH4) content in the reactor on diamond film deposition. The distinctive feature of the TMCVD process is that it time-modulates CH4 flow into the reactor during the complete growth process. It was noted that the substrate temperature fluctuated during the CH4 modulations and this significantly affected some key properties of the deposited films. We have deposited two sets of samples, where in each of the sets there was one sample which was prepared whilst the substrate temperature fluctuated and the other sample, which was deposited whilst maintaining the substrate temperature fixed. In order to maintain the substrate temperature constant the filament power was varied accordingly. In this paper, we discuss our findings in terms of the CH4 content in the reactor and the substrate temperature. It was found that secondary nucleation occurred during the high timed CH4 modulations. The as-deposited films were characterized for morphology, diamond-carbon phase purity, hardness and surface roughness, respectively.