Here is the list of differences through Stage 3:
A screen with copyright info plays when the game is started. I found a reference to this in
https://tcrf.net/Michael_Jackson%...) described as 'Unused Text'
When you start a game, there's a level select screen allowing you to choose the round and scene.
On the options screen the list of music samples is different, with generic names like 'Round 1', 'Enemy' etc. instead of song title.
There is no score & time screen after you beat a level.
The transition animation between 1-3 and 2-1 is different.
Bombs are always stationary and always explode after 3 seconds.
In 2-2 the two elevators at each end of the level are not synced. If you use one you have to go all the way back to it to change floors.
The 2-3 boss battle is different, there's no magic white dog, just a bunch of the regular dog enemies.
The Round 3 music is Thriller, the full song.
In the 3-2 and 3-3 boss battles you just fight regular zombies, they don't fly or detach their torsos or anything.