1) Mining missions
You were wise to try alt-shift-M. That is indeed the correct key combination. It seems it was a typo that I put alt-shift-A. Still, you said that doesn't work. I'll try it later this week when I have some time. To be clear you need to have a base as your alt-2 target and have to hold down the alt before the shift.
Found out why I couldn't make it work: I had a planet as the Alt-2 destination (the idea was to mine local resources for a newly colonized planet to build its spaceport).
Selecting a base as the Alt-2 destination works fine with Alt-Shift-M. Actually, Shift-Alt-M works as well.
While testing this, I also discovered another fact about mining missions: while it was already known that you couldn't normally mine one of your own colonized planets, nor build mining stations there, I thought that I had managed to do it anyway by using the Alt-M force order (what also gives the illusion of working is queueing a bunch of mining missions before the planet is colonized).
What actually happens, however, is that the miner reaches the planet, attempts to mine, immediately stops and goes to its unloading destination, without having actually mined anything.
Pity, now my miners have to trek across half the galaxy for some chromium and carbon fibre. Why is it that these so necessary and rare resources are always on the few good planets worthy of being settled? (Thus reducing their mining output).
Finally, I guess it simply isn't coded to have a repeating mining mission?
I have no idea but while we are here be sure you replace your decimal points with commas in the BaconSettings.txt file or you will get some funky results if you are in a country that uses commas as decimal points.
Got the decimal points sorted out at installation, you did put a very useful note at the top of BaconSettings.txt, thanks.
3) Alt-U destination
I usually give the freighter a refuel command at the place I want it to unload and then use Alt-U to make it unload when it gets there.
That's even easier, good idea.
5) The "guess strategy" minigame for ground invasions
I don't think I've ever invaded a pirate world. I'll have to look into that. At least your post gives confirmation that someone actually uses the invasion mini-game. How do you like it? Too easy? Too hard? Too boring?
Tested some more and I couldn't reproduce my own problem, so I guess that was a momentary interface problem or something.
Minigame opens up during any ground combat it seems, invade standard empires, invade pirate-owned planet, even during clearing of pirate facilities on a planet I own.
Took me a number of attempts to understand how it works. The bar at the top is how many attempts are available (filling up as I use them, though green is kinda unintuitive for that), gold star is correct guess in correct place, silver star is correct guess in wrong place.
My main problem now is purely graphical: the background image makes it somewhat difficult to comfortably read the text past the first few attempts, dark text on dark image.
As far as difficulty goes, now that I understand the concept it isn't too difficult, though I'll try it some more and see how it averages out.