Sounds about right. Whenever you start upgrading you find a lot of things to fix. Especially if you are the kind of guy who likes to have it right. I like a point to point amp better, but that is tubes.
I'm in favor of the 15 amp fuse. It won't heat up and will sound much better than a 3 amp fuse. If it isn't much trouble put in a 3 amp fuse and see if you can hear the difference. I bet you can.
Like you discovered with the black wires (good catch) many faults don't even run current through the fuse and the fuse is no help. But if it does, most faults will be much higher than 15 amp and will blow the 15 amp fuse. The only exposure is the "smart fault" that is more than the transformers (for instance) can handle, but less than 15A. Not gonna happen very often.
Great write up. Thanks for sharing.
Jerry
PS This is an excellent example of improvements that a talented technician can do to OEM work. Many members here have the mistaken impression that the OEM is perfect and to change anything is heresy.