Well, finally GadgetUK164 has uploaded the video fixing my Amiga1200 (issues mentioned in this thread), and he's done a fantastic job!
He didn't really discuss the Gotek, but the clicking is (obviously) the piezzo speaker emulating the disk drive. I later realised that it doesn't fit right as the Gotek has the front panel where the original Amiga's internal drive lacks one, so it is pushed back a couple of mm. I managed to fix it "properly" with cable ties, which looks surprisingly neat (when you actually look for it), and holds it securely in a good position.
Also, as I've mentioned in this thread - it's probably not a good idea to attempt surface-mount soldering for the very first time on a project like this. He's kind about my soldering, although does remark at one point "that is awful!" about one of my solder joints. I also didn't know what to do about the green / corrosion, and glad that he got that sorted. Didn't think after replacing them that it could still cause a problem. I wasn't even aware that any of the caps had originally leaked, as to my amateur eyes, they looked fine.
The keyboard connector was something that I had attempted to remove, and failed, only to attempt to get closer to the capacitors. Unfortunately I now have Kapton tape and a little more knowledge - something I would have liked to have known before I started. D'oh!
Anyway, I really recommend his channel. Thorough and precise - even if the fault I had was intermittent, and I think it took him quite a while before finding the issue. I also was completely oblivious to the sound issue he mentioned, and it's shame that wasn't captured on video.