I’ve tested it (Beta 3) on real hardware, specifically a PAL Mega Drive model MD 1601-18 with a stick mod, playing at 60 Hz on a Chinese Everdrive. I was able to finish it thanks to the invincibility mode. This time I selected Smooth ON. The helicopter glitch hasn’t shown up again, and neither has the muffled noise at the end of the stages. The bonus stages from the third one onwards (which I wasn’t able to complete successfully) loaded the ninja correctly. However, the first two and the one in demo mode still leave those strange tiles to the right of the ninja, which disappear after a second. There were three specific slowdowns: the helicopter, the next stage when a good number of ninjas pile up, and 4-1. There was one map (maybe 2-1) that came up in blue, but to be honest I was hammering the Start button like crazy to load stages, so I can’t be sure. At the end of the game, before the name entry screen for the score appeared, there was another strange load of black tiles that lasted about a second and then fixed itself. And one minor detail, just to mention it: when you finish the game, some letters rise up toward the portrait of the main character. The background is black, but the letters show through between the nose and the eyes of the character — something that should be black is transparent.
I hope this helps. Best regards.