Several things:
1. Agree with others there's no reason for the 3A jumper wire. Just run the Coyote power off the unswitched side of the master switch. BTW, when you say "ECU" I assume you mean Power Distribution Box (PDB) which is part of the Coyote Ford Performance harness. That's where the power for the system is supplied. The ECU is actually powered via the Coyote harness.
Yes, I meant PDB. I will run the PDB power from the unswitched side of the cutoff switch. I guess I thought I could power the PDB from the busbar and use the 250amp megafuse to protect more of the system. I read a thread where some people used the jumper to keep from losing ECU memory. Should I still use a megafuse or breaker before the busbar?
2. I'm also assuming the 250A mega fuse you're showing is the one supplied with the Ford Performance Coyote control pack? Per the Ford instructions, it's only meant to protect the Coyote system. Not the entire car harness as you're showing. That fuse should be between the battery power and the Coyote PDB.
Yes this was the fuse supplied in the control pack
3. You're correctly showing the Coyote SMR wire connected to the RF EFI crank wire. I'm hoping you mean the SMR wire in the pigtail harness. But that's it. That same wire does
not go the starter as you're showing. The Coyote harness has a harness leg (Item N) that goes to the small terminal on the starter. They're not the same thing.
Yes, the SMR wire in the pigtail. I wrongly assumed that the SMR wire was also Item N.
4. The Motorcraft/Ford Performance alternator recommended by Ford Performance (M-8600-M50BALT) is a 6G alternator. Hopefully that's what Mike provided. Uses the large battery wire, which you're showing, and is controlled by the plug-in connector provided as part of the Coyote harness. As already mentioned. The brown RF alternator wire is not used.
I will be contacting Mike this week to confirm. I can't tell from the internet if its 4G or 6G. The model #'s don't match what you listed. The plug for the alternator is from the coyote harness
5. You're not showing the complete Coyote wiring required. Maybe on purpose. But missing: Fuel pump, cooling fan, and ignition relay (required along with the SMR wire in the pigtail harness). Plus the dedicated stuff like the Coyote clutch pedal switch and DBW module (accelerator pedal).
Correct, those items seem straightforward so far. Although I'll probably have questions about the cooling fan when I get to it.
As an aside comment, sounds like you're using the Factory Five Coyote installation instructions. That's fine, and is certainly useful. I'd really encourage, if you aren't already, to also use the Ford Performance instructions
https://performanceparts.ford.com/do...-6017-504V.pdf. They have much more detail and explain the wiring a little better IMO. Between the two, should have what you need.