First congratulations for taking this big step to redraw a schematic. I suspect it was helpful to analyze your various modifications and get them clear in your mind. This is what real EE's actually do .
As drawn, you have many if not too many connections between the R/R and the battery. I count 15+ contacts or crimps. You can certanly reduce that.
Use the Revised Phase A tests to measure the voltage drops.
You should read up more on the SPG. If your R/R is close to the new fuse box then you can make the bus bar yoru SPG but follow teh SPG recommendations which you have failed to reflect in your comment so far.
You seem to have missed GS Charging health as well and you did not eliminate the headlamp switch loop, but did eliminate one stator leg.
On teh surface I don't see anything wrong with where you put that relay (assuming you get rid of some of the contacts listed above), so it seems you probably have too much voltage somewhere. Have you measured the voltage across the relay coil when running? Measured the current through it? You know it should be about 150 mA and not more.
I asked you before if you might have been using a stator leg to power the relay; since that leg is missing what did you do with it?
The image is also hard to read and I'm guessing you used 300 DPI which in my experience will not pick up the fine print. Use 600 DPI if available.
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