[Fixer]

You are doing a great job, I learned to weld 20 years ago on a B sunroof coupe restoration.

Your patch work looks very neat, i would acid etch prime the cleaned up area and the patch pieces, place the patch pieces over the prepped area and using a scribe tool scratch the outline. You can use a dremal to clean to bare (remove just enough primer) metal the edge of your patch piece and the area of the car which will receive the bead of weld.

You have to realize the heat will burn off some primer and there is really no sense losing sleep over that. Clean it up and re prime what you can see.
Inside it will last just fine when properly maintained as i am sure you will. You cannot let it make you nuts, it will be fine.

You can also buy special vise grip flange creating tool which will create an offset on the body of the car where metal replacement is to take place. It offsets the approxiamate sheet metal thickness to accept the patch piece and allow it to lay flush.

i think i bought mine thru Eastwood.

Best of luck