In the ONE foray I got into with a friend on an acquired 1950 Plymouth, in the middle 1970s, he rented a portable sand blaster to strip the orig paint and surface rust with. He got dressed up in the space suit to do the blasting with. Probably had too course of a grit sand, but the resulting metal finish was satiny. Everybody said just put primer on it, so that's what we did. Possibly a little thick of a mixture? So it sat outside to cure and wait for time to put the paint on. After about 2 weeks in the summer, little brown spots came up through the primer. RUST!
Primer is porous and not "sealed" like paint, so moisture will get through it, even from the morning dew or normal humidity changes.
There is a "metal prep" liquid for bare metal. I'd suggest that as an option. The people who grind to bare metal, for spot repairs, then putty or bondo as appropriate, then primer, then paint usually do it all in one day in a reasonably-controlled environment. NOT in segments spaced several days apart.
One of the weekend morning car shows, several years ago, recommended putting some paint into the primer mix, to help it do better.
Many who do paint/body work have their own tricks or what works with what paint, etc. That's part of what you learn doing that stuff. Similarly, each paint manufacturer has their own "system" from primer to top coat. Unless you know different, it might be best to follow the paint manufacturer's "system".
I strongly concur to get the body work done first. Put a coat of paint on it, to keep the lower levels sealed somewhat, then do the final scuff-up and paint when the time is right. Might use the black satin "primer"-look paint and then put the color on top of that? Just be careful of the ultimate build thickness of the total paint on the car. If too thick, cracks and crazes are more prone to happen as it ages.
Just some thoughts,
CBODY67