> Whenever I attempt to run this ROM in particular, it is running mostly at 75% speed
> and the sound is quite choppy. Same instance applies to the other versions 1.0 and
> 2.1. I don't understand why this seems to be the case as I can run other 3D games
> like Tekken 3, Soul Calibur etc. at 100% speed.
Tekken 3 and Soul Calibur run on original Playstation hardware, which is fairly cheap to emulate. MK4's "Zeus" 3D chip is more capable and takes more power to emulate.
> AMD APU A10-6800K Quad Core Processor 4.1GHz
That's your major issue - emulation leans heavily on single-core performance and AMD optimizes for multicore these days. An Intel CPU at 4.1 GHz would run MK4 no trouble at all.