The issue you're likely going to find is that PERHAPS (just speculating but it's been known to happen) that the original sealant dried up and pulled away leaving a tiny gap for rain to get through. This causes water to sit and find spots to rust out, further causing issues.
I got the feeling you're fishing for an answer that will tell you what to glop in there in the meantime to band-aid it. I personally wouldn't band-aid a water leak.
The sealant used was a butyl like substance that was put on like a giant glue gun, but the idea is that you most likely need to remove the back glass and repair any rust damage in the window channel. Then clean the entire channel and install the rear window with a butyl strip, carefully realigning the window back into its original position. Easier said than done.
If you pulled the bottom apart, did you break any of those special little umbrella clips? That's what holds the "chrome" trim on the bottom spacer panel between the window and trunklid. Most of the time, these get brittle and break. Need 8 of them for your Cutlass. I've got them if you need them. Lemme know and I can hook you up with GENUINE GM stuff. None of that chinesium crap the repros are made out of. I got handfuls of these. $29 for a set of 8 with a personal check. $28 if you pay with a USPS money order. Sorry, not using paypal anymore. But if you don't want to, that's cool too.
If you don't feel confident in your ability to remove/fix any rust/replace the back window, farm it out to the local auto glass shop. They can likely do it 100 times faster and then they'll be on the hook if it leaks. Or at least if they won't fix any rusty stuff, at least have them hold the glass until you can get anything repaired if needed, and they can reinstall it.
