Just got off the phone with the Ref. Here's what he said.
1.) Download and read the entire manual for the e-rod. Just follow all of the instructions and you will be fine.
https://www.chevrolet.com/content/dam/chevrolet/na/us/english/index/performance/resources/installation-guides/crate-engines/01-images/ls3-and-ls9-e-rod-crate-engine-control-system-40-tooth-and-17-tooth.pdf
2.) Double check the instructions. (Page 7 looks interesting, I'll need to take the car to a dealership for a test of some sort prior to smogging it.)
3.) As far as legality with the swap, totally legal and doesn't neccisarily need to be reviewed by a ref, since it is 1995 and older. He sited some CA law, but didnt get the full 6-digit code.
But he did recommend getting a "Virtual" referee appointment.
The call is setup so that the ref can talk to you over the phone as long as you need to assure everything is good to go. You can even go to them in person for a BAR sticker.
But with the EO (Executive Order) number that each engine comes with you should only need to show that to any smog shop in the state and they can run the car.
The big thing again are the instructions, as long as they are followed all they care about is the motor passing emissions. The manual states where the CATs need to be placed, but our setup requires them to be flipped, so that may be the only small let's find out area.
Going to dive into this once the car is at my house in the next couple of months and get this going.
I'll have a full thread of the build soon.