I can throw my A3000 against the wall and it will still boot. These A4000 machines are very finicky?
I generally find the opposite; the A3000 is full of low quality IC sockets that tend to cause various issues over time.
Anyway, sounds like you've tried pretty much everything you can. The 2nd CPU board you tried - was that a known working one?
If you run out of the options, I can have a look at the board for you. A couple of years ago I developed special hardware and software to report stages of software execution in A4000 ROM during boot which makes it possible to see exactly where the machine is failing during boot. Then it's possible to proceed with a repair based on the clues it provides.
http://amiga.serveftp.net