"1. Make it easy to tell from a console command or even the signal console itself which server has what upgrades. This QoL change would save so much headache for my completionist brain. Even if it's just a color change on each server's bulb to say if it's good or not."
Unless they removed it since version g, this exists. "sv.upgrades [server name]" lets you look up how many upgrades a specific server has. I generally use it to check any of the servers I need to visit for the day so I know how many I need to take with me.
Regarding the CR towers, I do agree they could use some sort of adjustment or change. I wonder if they might work better if they were more like the transformers, where they had a numerical value to determine how much integrity or whatever they had remaining, so you could just check it via the console each day and if one was running low, you could just run out there and reset it or something.