#1
Im confused, with all this theory stuff, I dont know where to start, fist I learned the notes on the fretboard (not memerized, but i can find certain notes), but I dont know how I should learn scales or in what position, so could somebody please tell me what to do?

Now im an high intermediate player, and I know what im doing playing, I can play very well if I may say so for myself so I really need to kick it in gear and learn how to improvise and do this and that, but im very confused
#2
Ummm first off. If you are just learning the notes on the fretboard you are by no means a "high intermediate player". Even if you can play every single little AC/DC, or Van Halen (or whatever else 13 year old boys are obsessed with now) song note-for-note you are no means a intermediate guitar player. You're simply a regurgitator. Go on Amazon and find a theory book. Mel Bay makes OK stuff. Go find it now.
a little lie says you'd like nothing better.....
#3
Try making pedal tones with the root notes in scales. That's a good springboard for improvising solos and things.