Can you help an evil brother out?

I've been playing for a month now and upgraded to TWA last week. I have to say that this is one of the most enjoyable and definitely the most addictive game I've ever played. I was still playing Master of Magic until I picked this up last month, lol. The game is lovingly crafted and it shows. Almost every time I have had a question, or thought there was a flaw in the controls or handling of the game, with a little thought and patience I have been able to figure out how to get the game to do what I want. With two great, big, pain-in-the-butt exceptions. I hope that others may be able to help me here. I have seen other people complain about these problems but that was earlier when I first started playing and didn't understand what anyone was talking about and now I can't find those posts again. If someone has advice or a solution that has already been posted I certainly don't mind a link back to where that solution is. Here goes...

#1 Auto-upgrade of improvements. How the heck do you turn this off globally? I was in the middle of a fearsome battle with the Torians, doing quite nicely, when I took one of their planets and got the industrial sector tech. Blam, my whole empire goes into gridlock for the next 50 rounds while my manufacturing plants are being upgraded. In playing around with the governor option I can see where I can designate each new planet to not auto-upgrade, but frankly that is a PITA to have to remember to set that feature every time I take a new planet, not to mention time-consuming and clunky because the option is buried about three screens down and just involves too much clicking. So, is there a way to turn off auto-upgrade globally?

#2 Defending starbase mines. It sure is nice to have those research, military, and other special resource nodes contributing to your empire. It sure is awful to see them disappear in a puff of intergalactic debris when some nasty alien culture decides to sneak attack you. To defend my starbase mines I have found the best way to do so is simply to park one of my decked out fighters on top of them. This seems to be more effective than investing thousands of research units into the tech tree to build decent defenses on them, not to mention the thousands of credits spent on constructors to build those defenses. The only problem I have is that when I park a fighter on top of my starbase mine, at the end of every round the game prompts me to move my fighter.  I tried creating a fleet using the fighter and the starbase, that doesn't work, and when I set the fighter to guard or sentry, the game still keeps prompting me to move the fighter. Every round. Times 5 or 6 starbases. Every round. Over and over again. This becomes a big PITA and detracts from the enjoyment of the game. I want an option to have my fighter guard the base without the game reminding me about it evey single turn. Can anyone help an evil brother out here with some advice?