I had the same issue with the cowl needing replaced.
My Challenger was a rust bucket.
I have pictures during the re-body experience. I am keeping the original cowl and storing it in the attic.
I have a title to the car with the correct vin and my core support has the numbers on it. That is the only place left on the car with a stamped number on it.
I don't think I would go cutting, welding or stamping numbers on the car. To me that's raising a red flag.
If you are concerned, talk to your state troopers or licensing professionals on how to properly "mark" your car with the numbers.