It is usual when starting a run to use the most recent stable version of the emulator.
Although SNES9x1.53 has been released there seem to be some problems with it that haven't been resolved yet.
I would suggest it is best you use v1.51. Don't worry about the previous movie being made on a different version of the emulator, that is irrelevant.
But you say that "the ending" is glitched on this version. What is the glitch?
-If it occurs after the end of your input it doesn't really matter I think.
-If it occurs earlier during your input and is something that cannot be reproduced on the actual console then it is best that you wait for a judge or administrator of this site to advise you before you start the run. They will need you to describe the glitch in more detail before they can advise you.
Whichever version you decide in the end, let me say - good luck for your run, I look forward to seeing it.