To get on the right runway, set everything up and then move down the taxi way. You will here runways beeping with an audio name on the left or right depending on where they are, that's if you're using headphones of course. Slow right down when you here the sound for that runway loud in one ear, let's say it's the left, and then do control left arrow to turn onto that runway. You will hear the runway moving until you ligne up with it and then you will get a ding to say you are straight on it. Assuming you still have long enough left on your clearance, then you can just take off normally from that point.
As for repeating commands, it's the space bar. press it to have the last ATC instruction repeated.
With things being a little out with altitude and navigation... yep that's annoying many people I think. It's partly because of the joystick support they added, it's more sensitive for those who use a joystick. I think their may be a way to change that in some config file so it doesn't use the joystick mode, i'll look into that for you. As you advance through the game though, you will fly more advanced aircraft and they will have some auto systems so you don't have to handle altitude and navigation by hand, although as their isn't much more to do in the game when in flight at the minute that can get a bit boring.
To the person who said about the runtimes, well I really don't know. Never experienced that problem myself, all I can suggest is uninstalling the game and reinstalling. If that doesn't work then ask the DEV, although I doubt he will reply sadly as he doesn't always do so.
Declan.