Hey ive been playing for 2 years. I really want to get to the point where i can improvise and just naturally flow the notes im hearing in my head out on the guitar. Ive (sorta) memorized the notes on the fretboard and am slowly getting used to how they are going to sound before i play them. Everytime i make up a little riff in my head, it takes a while to play it on guitar. So, how long did it take for the improvisers out there to just play along and play whats in their head while matching the key/chord changes, etc... Besides scales and theory, any tips? thanks!
Not just knowing scales but knowing which scales sound good over which progression and which scale you should use for the sound you are looking for
experiment a lot. eventually you'll know what works and what doesnt over certain chords/riffs. i found watching other/more experienced players really helpful. try playing with a lot of different guitarists and pick up bits and pieces from them.
It took me years to start being able to do that, and I'm still only part of the way there.
Actually called Mark!

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It depends on the person, for me... it came pretty quick. When I first started I would pick some simple song... like the melody to danny boy... and find the first note! For me, it comes naturally to know what fret to go to next! But, for some people, familiarization with intervals takes longer! If I were you, I'd work on aural training! So, just practice I guess!
The reason most great improvisers are so...great...is because they have formed an amazing amalgamation of influences ranging across multiple styles.

Take Eric Johnson for instance. On his DVD (you can find clips on YouTube: "Total Electric Guitar"), he discusses this topic in great detail.

My advice: Don't be lazy. Sit down with a record and transcribe (if you cannot read music, this is somewhat excused) various solos that you enjoy. Learn every lick by ear, ignore tabulature for now.

#1.) Play with other musicians. Just do it.
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I recommend you practice up on your scales, especially the minor pentatonic. Sit down and listen to a song you enjoy and then play these scales over top of the song. Listen to how the scale sounds especially how the way certain notes sound over the chord changes. Then experiment playing sets of the notes at different times in the song. Eventually you'll hear patterns and develop the instinct for improvisation