Lower rear window water leaks/rust is NOT a Chrysler-specific issue as GM full-size cars of that era had a much worse situation. Enough so that 3M invented "AlumaLead" to plug the holes with, early on. Chryslers took much longer for that to happen as they obviouisly put more body paint in that area and the paint was acrylic enamel rather than the GM-use acrylic lacquer.
Those sloped back glasses look neat and aero, but they also provide a dam to stop run-off from getting to the deck lie surface. Which means water puddles under the moldings until it might evaporate. Over time, the paint deteriorates (lacquer faster than enamel, typically) and things progress from there. Vinyl roofs probably don't help as the backing of the vinyl material can absorb moisture, too.
Learning of the GM issues, when we got our new '72 Newport Royal 4dr sedan, after it had been dry for a long time in the summer, I got some black "dum dum" seal caulk and went around the vertical and horizontal rear window molding sections, putting a bead of caulk between the moldings and the glass. Then tooling the caulk with a pop sicle stick so it all looked nice and incognito. I also left a few little gaps in the vertical areas for vapor evaporation. No vinyl roof, either. And my efforts paid off. A bit less wind turbulance around the moldings and water had to work to get under them.
Other than the rust areas chronicled in an older thread, the ONE item that many might not even worry about is factory a/c case condensate leaks. I was at the local dealership one afternoon when the dealer was talking to a customer about how they'd get her '69 Fury's water leaks fixed. I later quietly asked the old-line Chrysler service manager about that issue.
He related that they deleted the drain pan and that left the gasket between the case halves as the main sealing location. I knew we never had any issues with our '66 Newport and worndered why the new '69s might. Later, after we'd had our new '72 Newport Royal for a while, the front carpet was getting damp and water was getting on my mother's shoes. So it went in for an a/c case re-seal. It was fixed for a while, but came back. Several years later, I removed the factory floor mat on my '70 Monaco to find the carpet under it was very damp.
On the surface, it looked like the seal should do a good job as they used to. BUT then I noticed that the metal slide-over nuts were compressing the gasket as it tried to seal against them. Leaving little gaps on each side of the nut's width. More tightening torque would not help as the gasket's surface was a bit stiff. Using flanged-head bolts (or some with a captive spring flat washer) to connect with similar nuts on the backside of those case halves would have worked much better, but more assy time on the production line. So production ease and decreased costs probably took precedence over longer-term customer satisfaction?
In more modern times, some dabs of black high-heat silicone on the flat areas of those slide-on nuts, plus a skim coat of sealer on the inner surfaces of the seal gasket, with NO sealer on the passenger compartment half of the case would have probably worked just fine. Long term. Sorry for the length.
Any time you need to do a front pump removal, much better to drop the transmission (might still leave it secured to the trans jack, though) for better working room and such. NO need to "fight it".
Just some thoughts,