Clean around the holes on the backside and fiberglass mat to waterproof. Then bondo the topside. This will be easy and last a long time!
Fiberglass and metal do not mix. Bondo absorbs water if not
completely sealed, and sometimes even then. This is a recipe for a giant rust hole. Maybe not for a few years, but this is not a permanent fix.
Fiberglass used to repair metal or bondo used to fill holes are shortcuts. It's not the right way to do it, it's not a permanent way to do it, and eventually it will cause even more work than there was to begin with.
It’s definitely going to take some practice. But it can be done on a vertical surface? I’m trying to get them all filled before I prime the car. A little nervous about the holes that lead into the interior, last thing I need is to burn down my car with an fire started by hot lead dropping down into somewhere unseen.
Lead can be used to fill small holes. It would be a heck of a lot easier if it were laying flat, but it can be done vertically. But if you're not a skilled lead slinger, it is going to take a lot of practice to get it done.
The other problem that you're going to have is that once you're done applying the lead and shaving it down with a body file (don't sand lead!), there won't be much lead left on the top side because you're filling a hole on a flat panel, or worse, on a body line. That can cause adhesion problems, and may cause the paint to crack or the lead to lose it's bond with the metal.
By far the easiest way to do this would be to borrow/rent or even buy a small 110 MIG welder, just get one with an gas set-up so you don't have to use flux core rod. The amount of practice/time it will take to you to be able to do a good job welding up the holes in the sheet metal will far less than what it will take to get the lead work done.
Also- are we just talking the holes at either end of each trim piece for the screws? Or the holes left behind by all of the studs? The studs were spot welded to the body, if you remove them with a grinder and cut off wheel they don't leave holes. The studs only leave holes if they're pulled off, because then they take the base metal with them. I have to do this repair on one side of my EL5 GT because some jerk pulled off all the studs. When I converted my Duster over to a '71 Dart front end I used a grinder to remove the trim studs, no problemo, no holes except for the one at either end for the screws.