New Fuse Box Questions

The black wire is thicker than Painless' pink wire yet you are worried the black can carry less current? Try editing.
2 series fuses aren't needed, but wouldn't hurt.
I would used an in-line fuse since more accurate and easier to replace. I think I have seen them up to ~80 A at auto parts. Fusible links were a cheapie factory design to avoid catastrophies. Some cars have a fuse built into the BATT+ connector, so there might be retrofits. That would protect for most things, but might also want one on the ALT+ output wire.

Any 12 V source would work. Why not BATT+ which is just above your relays? Much easier and safer than the circuitous route aft to the firewall then fwd again. The only disadvantage is that if tapping BATT+, the current used won't be measured on your dash ammeter, if still using that. Indeed, no under-hood loads are measured in the factory design, but they are all transient - horn, starter, ...