The audio splicing is briefly mentioned in this video.
The biggest red flag is the way the screens are loaded, and that has been the biggest talking point. Basically, arcade loads each screen transition in a way that only happens on the original hardware, and the MAME transition shows it differently. This is something that happens 100% of the time on each platform and there is no crossover, meaning there's no way it's a fluke.
The idea was floated that perhaps he was playing on what he thought was original hardware, but it was really just an arcade cabinet with an emulator inside. The audio splicing, mathemetical issues with his scores and a number of other things show he definitely cheated and he knew it though. For example, he frequently stated that he had no idea how the arcade cabinet worked, yet was somehow able to capture video footage directly from the "arcade machine" to submit to Twin Galaxies, rather than pointing a camera at the cabinet. It is impossible to capture video directly from a cabinet without an intricate knowledge of how the boards work.
Do you have a link to the spliced videos?