I'm kinda in your same boat but about a year and a half along. What I found out real quick is that as great as youtube and websites with lessons are, books are where it's at.
I started with How Music Really Works. The information in it is pretty simplistic, but aside from a few liberties taken(ok, a lot!), it'll give you a pretty good hold on basic music concepts and open the door to things. Think of it like a pre-cursor. Like Highschool Music Theory or something. Just don't go around trying to communicate with people until you've read a few more formal books.
A Modern Method For Guitar is pretty essential. I'm through volume 1 and between that and Tonal Harmony as well as Arpeggio and Scale Resources (that one's free online!), I have a much better grasp over reading and understanding basic theory and working with standard notation.
I think someone mentioned ear training and sight singing. I was in disbelief at how much those two things actually helped when I started learning them. Not only with reading music, but with being able to just hear something on the radio and know what's going on. Do it!
It also helps to try to find what books are used at places like Berklee or written by their students/faculty. I recently went through a few books by Pat Pattison (basically established Berklee's Songwriting major) ( Songwriting: Essential Guide to Rhyming and Writing Better Lyrics ) that helped immensely with my lyric writing and songwriting overall. I also read Popular Lyric Writing which expanded on some of Pat's stuff.
'For Dummies' books are also pretty helpful in getting the wheels turning on new subjects.
Anyway, that's only really a few suggestions but I'm tired of finding amazon links lol. I acquire my books by..um...alternative means, so I have A LOT tucked away in a folder and I've probably burned through ~30 books in the past year and a half. If you put in the time, you'll learn. Practice too! Like FO REAL PRACTICE! None of that noodling while you watch TV crap. Hit the metronome! Also, don't forget to get out there and play in bands and apply all that knowledge. And also don't forget to be a sponge while you're out there doing your thing. If someone you meet knows how to (blank) at a professional level? Make them teach you.
The bottom line is that self-study is no joke. It's a bitch. It's slow. And no one's going to be able to really help if you get stuck or aren't understanding something. If you're up for it, I can say from personal experience that it's possible.
I ended up getting singing lessons about 4 months ago because the self-study isn't working out with that as well.