Here is what I could give as advice.
First, here's the stuff everybody can tell you, start slowly and then build up the speed playing with a metronome (or Guitar Pro, that's a nice tool). Now, here is some precisions. It doesn't matter what you're playing, it's going to work for any exercise. If you want to start practicing your scales that's fine, but you can do it with any exercise you want to develop. Find some small exercises and play them in loop. You could write it out on Guitar Pro and put some repeats on it. Try playing it for a whole minute without stopping. The idea is to feel it working in your arm muscles. If you can do it for a minute, do it faster. You can aply this to any exercise. It could be a part from a rhtyhm section, a solo lick, anything you want to play faster. It's like a workout, or a weight training program. You got your exercises (the lick), The weight (the speed), and your number of reps (the one-minute duration), and then the muscles have to hurt!
For playing by ear, you can use a similar process, start with a small part. Listen to just a couple of notes then press the pause button, and find those notes on your guitar. Listen to the following couple of notes and press pause. If you are fast enough with the button, you can hear only one note (even in fast passages), and that makes it easier to find. And don't worry, the more you do it, the better you are at it. We all suck the first time we play by ear.
Hope this helps.
Marc-André.