1) I didn't see the connection from the alternator to the battery...the fuse is there, but I didn't see the connection to the battery!
2) Fuses are usually sized to protect the wires. Do you have the 1GGZE wiring diagram with fuses sized? If not I'd probably look to use the 1GGTE fuse sizes.
Also you don't need a separate fuse for the two COR relays, you can just use one. Think of it as the fuse to the fuel pump. Usually about 10A to 20A depending on the pump.
In addition there is normally a fuse for the alternator Sense wire close to the battery (see link below...).
3) Link
4) Have a look at the earthing for the 1GGTE, normally the intake manifold, engine block, etc are earthed also, and this is important. I don't see an issues with what you've described at a quick glance...
5) I can't think of any circumstances in a car when a relay with an inbuilt flywheel diode is likely to cause issues. That said I don't recall ever seeing a Toyota relay with an inbuilt flywheel diode, so not sure there is a need...
Some other notes:
>The engine EUC IGSW wiring doesn't look correct on your drawing...
>Not sure what is going on with you SC wiring (I've never had to look at this personally..), not sure it is correct?
>NSW wiring
Cheers
Wilbo
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