This throws me a bit ... are you saying the FDD continually spins up and down? But if you remove the logic board, how can the sound continue if the FDD is no longer connected?
If you have the Pina book, then you have all the information available on the Flup assuming it's not multiple problems and you are diagnosing it correctly. I would do exactly as you are and go through each one step by step.

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The CRT makes a whistle in time with the FDD. The whistle continues even when the drive is disconnected.

I don't have the Pina book, just a few pages scanned from it.

I've replaced the 200v HV capacitors and there's still no change. I've spent $70 AU on this thing now for no result, so I think it's time to give it up and let it die.

EDIT: We have power. The flupping is gone and the CRT is now getting a charge (it sparks when I discharge it). However there's still no video and no chime. Getting closer though, maybe a few more flows of the analog board will have it working.

EDIT 2: Sad Mac Baby! Time to get to work on the logic board. Unfortunately the code below the Sad Mac is garbled, so I can't read off what the error is.