So I've been playing guitar for about 2-3 years and stopped taking lessons after taking them for 3 months. I know the general structure of major/minor scales and the 5 minor pentatonic shapes but I'm feeling confused right now as to what I should learn.

I can't play every major/minor scale and I haven't memorized all the notes on the fretboard but I don't know what I should be doing to get the ball rolling. What exactly should I be looking at now? For example what can I play to really understand the major/minor scales? What exercises are there to memorize the fretboard or does that come naturally as I learn more scales? What scales/techniques should I learn next?

I'm willing to learn but I just don't know where to start from here.
Just trace back, step for step til the beginning, and then start over again, basics and whenever theres something you have to think twice about, learn it to perfection. Also, try to write your own stuff. You learn a lot of things there
Thanks for the fast response, in terms of scales would you recommend practicing them one key at a time but in all positions, or one position at a time but with all keys? I've been looking back at the basics every now and then but haven't really dug in deep enough. Thanks for the advice.
Honestly I think the best thing you can do is apply what you know. Do make sure you know the scales/modes, but go find tabs for some songs you like and learn them. Not just learn to play the tab, mind you, but look at how it is put together. See what intervals are being used and how they sound, and try putting together some sort of improv solo on top of it if you think you would enjoy it. It will be very hard at first but lots of fun the whole way, and you will realize after a few weeks that you understand the fretboard much better than you thought you did.

Speed will come naturally as you play more, and you'll be able to write/play more and more easily as you get more comfortable with everything. The main thing is just to play - don't worry about exactly why because that will probably bore you and make you take breaks when you may not otherwise have even wanted to. Enjoy it, and you will progress fast!
Start writing & find a band, preferably with another guitarist. You'll learn from observing someone elses technique & sound, and become an overall better player.
You know, you're probably reading this saying "Hey, I'm bored, maybe this'll be funny?"
It's not. Too bad. No, I am not refunding you those 6 seconds of your life. So :P

Don't think of the scales as shapes. Learn the notes of the scales and the notes of the fretboard. Then you will have the freedom to move around. Other than that, pick a song and start learning.
Quote by Geldin
Junior's usually at least a little terse, but he knows his stuff. I've always read his posts in a grouchy grandfather voice, a grouchy grandfather with a huge stiffy for alternate picking.
Besides that, he's right this time. As usual.