Hi.
The most important thing to learn for a newbie is to know when you are screwed. This isn't just at the points that make you go 'AHHH HOLY SHIT', but also at the points that make you think 'Hmm... this looks tricky. I wonder if I can do this?' The 'I've beaten this once or twice before... it would be cool if I beat it in an actual run' mentality CAN AND WILL KILL YOU. It still kills me all the time.
If you are unsure, BOMB. This will allow you to get much further in almost anything (having said that Flandre is invincible against bombs for most of the battle so you'll need
some dodging skill :V).
Also, use and abuse Stage Practice. If something is giving you a hard time, practice that section over and over until you understand it (or you can designate it a spot where you need to bomb if you're lazy like me, but understanding it will save resources).
In terms of the stupid mistakes, you'll just need to play more and get some more experience. Stupid deaths happen to everyone and the only real way of preventing them are general good dodging habits that will kick in when you're not really paying attention.
In terms of EoSD, I would strongly recommend you manage a Normal 1cc of the game on default lives before you attempt to beat Flandre. It'll improve your skills, and a Normal 1cc is
far easier than a clear of EoSD Extra. Flandre is tough. Most of her cards are on par with Hard/Lunatic level attacks. I would also recommend
against using MarisaA for the 1cc, as she has a really, really hard Patchy fight.
Also, if you haven't already done so, get the vsync patch. Do everything you can to make it work. You may not notice it at first, but it will do wonders for your dodging. It basically removes the input delay from some of the earlier Touhou games, effectively giving you better reaction times. Too tired to explain setting it up, but all the explanations you'll need are in the Tech Support section of the forum.
I have no idea really about the keyboard mapping or the key limit problems. Sorry. :V
Finally, you can't expect gigantic leaps in skill every time you play the game. Take your time, take breaks if you rage, and don't give up. You'll be 1ccing the games left and right in no time.