Yeah Bill, that’s seam sealer. I use a wire brush on a drill to take the old stuff of my panels. You’ll find that in areas under the hood as well.
You’ll want a good two part “epoxy” style seam sealer to replace it with. Flowable seam sealer is the best to use, but it’s a pita when doing the curved areas of the door, it flows back along the curved sections and wants to
puddle in the center area. I used a heavy body seam sealer on the doors for that reason. It takes a little more work to make it lay out nice.
Here’s a picture of my hood when I masked it to seam seal. I’ll come up with a couple more pictures in just a little bit.
The seam sealer helps, believe it or not, to prevent rust along the entire edge. It causes moisture to be directed towards the weep holes.
As for more weep holes? You can, just make an elongated hole similar to the factory holes. That helps to prevent blockages from larger crap.
You’ll want to get some sort of corrosion protection spray inside the panels along the bottom areas to seal up from the inside too. Nothing difficult there, you can use the same stuff that I spray inside my frame rails. You can find a parrafin type that has a little plastic wand that can direct the spray where you want it. There are other things that you can use as well, like POR 15 (rust encapsulators).
You can paint your car with the panels on or off. Though it will be easier to paint everything off so you can avoid having tape lines in the jambs. If you go that route, be sure to put tape along all the edges before mounting the panels after it’s painted so you don’t scratch anything during reassembly. The hatch would be easier shooting off, then you can paint the jambs at the same time as the outside. Nice and smooth that way.
I’ll post more pictures here shortly along with a little more explanation on painting.