I am confident based on your responses what you have done so far that you will find the wire/cable that is grounding!

Good hunting!

 

I experienced a similar thing after an engine swap — it was a poorly fixed ground cable that caused a short circuit and blew the fuse. The whistle came from a stuck relay. Check all the masses well and if the starter/alternator wiring is reversed. Good luck, I know how frustrating it is.