You might try doing this in two passes, in future. Try simply playing the chords ONLY the first time, and making an SMF of the backing (which might allow you to use FULL chord recognition and ON BASS (Bass Inversion ON) to do it with two hands, and this might clear up a lot of the shakiness in the bassline.
Then add the theater organ stuff as an overdub...
It's fun to try and pull off things like this in one pass, but if the end result is a bit shaky (there are sections with a new chord almost every beat, tough to pull off and play RH too!), there's no shame in using a bit of studio trickery!
Definitely took me back to my Butlins days!
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An arranger is just a tool. What matters is what you build with it..!