In this work, we analyze the effect of residual frame timing offset and carrier frequency offset along with the presence of fractional Doppler on the bit error rate performance of OFTS system. We show in this work that channel equalization with appropriate channel estimates can compensate for the combined effect of the time-varying multipath channel (TVMC) as well as residual synchronization errors. We also present a unique time-domain channel estimation method for OTFS, which can be used along with the above-mentioned channel equalization. It is seen from the extensive Monte Carlo simulation results of the LDPC coded OTFS system that the estimation and compensation methods presented here provide necessary resilience properties to OTFS against the effects of TVMC channel and residual synchronization errors. A unified signal processing flow for OTFS and OFDM is also described in this work to motivate studies on coexistence between the two as well as to encourage investigations on a seamless transition from OFDM based system to OTFS based systems for future air interface design. This Work is submiited to an IEEE Journal for possible future publication.