I just replaced 74HC04 with 74HC14 (Schmitt trigger) in my driver board and now the motor movement is smooth, no noise and no missing pulses at all. Like gliding on oil
Only remaining issue (apart from those little general and not very important comments on SS software) is cooling of the driver module - I will sort it out with heat sinks and couple of thick silicon pads (for better thermal contact).
And, before I forget, it is worth mentioning that I also shorted R4 (10k) resistor on pololu board, marked with blue arrow on image below. This is to remove the missing pulses issue (more details are in data sheet for A4988 chip).
Very happy !!!