You have several issues here obviously, the leak and the rust, so let's address each one separately.
THE LEAK: If it is leaking in from around the window, you more than likely have rust in this area or something else happening. Short of removing the rear window and resealing it (best course of action), you need to pull the trim and seal the entire window, I would used butyl sealer as that is probably what is holding that window in right now (assuming its original). If the window was installed using urethane, then you need to use urethane sealer. If you put butyl sealer over urethane or the other way, they don't usually seal.
You might want to take a hard look at the trunk weatherstrip (seal) while you are at it, it maybe possible that it is leaking under or over it.
If you want to actually find the leak, pull the seats our to include the backseat, you can then get in there and look while someone else sprays it with a hose.
THE RUST - the market is full of miracle cures for rust, the only real way to get rid of it is to grind or cut it out, but if this is spot or surface rust you can deal with it. You need to get as much of the flaking part off as possible, then you have to neutralize it. You can try any number of products ranging from Naval Jelly to an acid solution. If you are serious about it, you should look at something like POR15, KBS, etc. that is designed to neutralize and encapsulate it. Bottom line is that if you cannot keep it dry, this is going to be an ongoing issue. The rubber trunk mat is not your friend when it comes to this issue, it not only traps the moisture but its concentrates it at low spots not allowing it to evaporate or spread out to evaporate. I would definitely remove the mat until you get this leak deal sorted out.
I apologize in advance if I am telling you things you already know or have thought of; just trying to offer a shotgun blast of information that I hope may be helpful in some way.
Thanks for the feedback!
So, I tried to find leak again since the fish was in the driveway, the sun was shining and the trunk was empty.....closed the trunk and hosed her down.
Found it. Er...them.
Looks like the lower rear window seal is leaking like a sieve.
I have water on my inside package tray, along the entire bottom of the window, and it is funneling into one of the speaker holes on the left side.
That goes right into the trunk.
That's the primary leak.
I also have two small secondary leaks, where the Dutchman panel (??the panel between the window and the trunk??) meets with the fenders. It's a seam. Just a drop or two there.
But enough to cause water.
I had once tried to seal the rear window years ago, and I thought that I had gotten it. Used silicone around the lower posts/screws for the window trim.
But I guess I didnt get it....... not sure if its the window seal or the trim studs again??
So I suppose the window has to come out, all of those holes and studs have to be addressed, and then the window put back in.
I would have to run it down to a glass shop I guess and have them pull the window. and pray that they do not break it pulling it out. fix the stud holes, and then have them put the window back in and hope that it doesn't leak.Sigh.
In the meantime, I stripped the flex seal off of the trunk floor, and got it all down to bare metal in those areas. I would say it is about 50% of the total floor area.
Left the rest of the trunk painted as-is. there is also some very light overspray from the leak seal. I will never use that crap again.
Used afterblast to temporarily protect the bare metal from moisture and flash rust.
Went to home Depot and bought some indoor outdoor carpet, cut it to match the mat, and put that in instead. It will breathe much better. hopefully that will be a temporary help. Either that, or I will have to drive the car in a bubble. LOL.
Will leave the afterblast on it, and check it every week I guess. Reapply it every couple weeks. At least until I figure out what I'm going to do.
Paint might hold up better under the carpet rather than under the non breathable rubber mat, but water is still going to get in and sit there so I am not sure I should bother yet.
Glad I do not drive the car in rain very often and its stored indoors. But it does happen, and it's a pain emptying the trunk every time it rains.
Ah, the joys of owning an old Mopar. Lol
I will try and upload some pictures I took.....I used a big mirror and laid it in the trunk....the bright daylight helped me see stuff real well but not sure how the pics turned out.....