The late 240Z had both a mechanical and an electrical fuel pump. There is actually factory wiring for the electric pump in all of the 240Zs I believe. I know that my 71 had wires in that location that go to an un-used connector.
I don't know what the MSA setup entails, but I do know that the later alternators are internally regulated so using your original voltage regulator is not possible.
I don't have any details that would explain why you only heard the "clicking" sound after the alternator upgrade. Check with MSA as they may have encountered this phenomenon before.
I believe that the adapter they provided may have been made by someone here on this site. Perhaps they can chime in. (Sorry, I can't remember the name at the moment.)
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