I couldn't find the sales numbers by engine, but in some of those years the Mustang won by 2X all the way to 4X. Unless Ford sold almost no V8 models those years, you cant blame it on base model sales. I've always wondered why the Camaro was beaten so badly by the Mustang in the 4th Gen years as the Camaro very much outperformed the Mustang in the V8 models those years. It had the beautiful Chevy 350, while the Mustang had the 4.6 2V which was not one of Ford's better V8s. Not to be a jerk, but since you claim it was due to V6 sales you should be able to provide the sales figures.
I'm not even sure why people hated the 3rd Gen+ hatchback design. My buddy bought a new 1991 back then. Not only was it more convenient compared to the small trunk you found in coupes, we also found that the hatchback design was perfect for putting a pair of subwoofers back there.