OK, been hitting the wiring hard the past couple of days. Since I have never done ANY wiring, its taking forever. Spent the time cutting out what I need for the new stuff and detangling.
I am trying to use notes and instructions from other folks. I think I understand most of it, but in the diagram below, I tried to capture the parts of the wiring that I don't quite get or have questions on. Specifically, it is with the ignition wiring, alternator, etc. and how to tie in.
So those who have done this or know what you are doing...how does this look? I am sure I have a bunch of stuff wrong. One of my big fears is that I don't understand some wiring basics and I will wire this to explode

. I am using 73tlcv8's suggestion of a new switched relay to the ECU. Anyway, can someone help me out here? How does this look, what is wrong, etc.
Just pretend I am an idiot when explaining to me, and I might understand.
Specific questions I have:
1) For the alternator, should I instead be using the existing alternator wiring? For this, I basically took the alternator wiring from the 62 diagram and plan to recreate it in my 40. Also, the alternator has a YW wire for a "charge fuse"...what is this?
2) The IGN Main Relay has two wires that go to fuses...engine fuse (BL wire) and gauge fuse (Y wire). Can I just tap these into the FJ40 fuses for these purposes?
3) For the new switched power to the ECU, one of the wires went out to a fuse...not sure which fuse and what the purpose is. (this question maybe for 73tlcv8 since I am using his notes).
4) I plan to keep my FJ40 fuse box and add inline fuses where necessary. I count only two of these - an ignition fuse between the relay and ECU and an EFI fuse. Both are on the diagram.
5) Are relays all the same? Meaning, can I take an unused relay from the 62 harness and convert it for my purposes here?
6) I cannot find the alternator fusible link on the 62 harness. Are all fusible links the same?
Thats enough questions for now. Thanks.