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Peter,

The second point in my OP has still not been addressed. Any changes made to a Reports CPT do not save. Max_input_vars is already at 10000, and I did not have an issue saving this many fields using ACF.

Could this be an issue with the custom tables setting?

I have just checked the site, and even with those plugins disabled, it took over five seconds for the edit page of the CPT in question to load the fields in the first tab. Switching tabs is still taking 3+ seconds.

To be clear, I'm experiencing these issues both on a staging environment that I cloned the current site to and ran the ACF Migration plugin on as well as a brand new installation that I've imported the fields from the former staging env onto.