The 3 large holes required were for if you wanted to remove just the motor from the regulator assembly and give access with socket. I guess they thought it was quicker to do and less work during a quick service or repair, not a restoration.
I did mine when I got the car 20 years ago as a young fella, drilled the rivets out, lifted the glass and regulators out to swap in new window motors. I replaced with bolts, with the heads soldered into place to create studs. They only need to hold them in place until you can get it back into the door as was a bit fiddly getting them in with dropping them each time. Years later they are still intact, but I'd do something different next time, not sure what yet. I hardly remember doing the job, did most my work during work shifts through the night when not sleeping. Limited diagrams, manuals or info, just went with it. Of course, the job made no difference as the original motors were fine, it was just the typical Firebird worn-out electricals so later they were rewired with relays.
Where does the noise come from? Window guide blocks work out? Dried and scratched up tracks? Gouged up rollers? (Although called rollers, they don't roll, they only slide) There's also a lower felt guide at the top one of the channels that wears out and often not replaced. It is located near the mirror mount.
There's a few youtube links to guys replacing regulators that may be of use. This one is a manual regulator.
https://www.youtube.com/watch?v=hI28WEb-aw0
