So yesterday I had guitar lessons, last week he gave me some simple stuff. This week he asked me what I thought so I said 'pretty easy' then he gave me a really complex, almost college level Music theory lesson. What I 'deduced' from this lesson and my own mind is that the chords that fit into say G Ionian are the chords you would play to accompany lead guitar. I also figured based on that, that all the chords that fit in the mode say a G chord could be played in the inversions on other places on the guitar. Is this correct? I know there are extra rules in some cases but am I somewhat right?

PS. If anyone knows any good music theory books or websites for guitar that would be great, something easy to follow.
Not sure exactly what you're asking. First of all, let's not talk about modes. If he tried to explain modes to you at this stage, he either a) doesn't know what he's talking about or b) knows what he's talking about but is unnecessarily complicating things.

The chords you produce from harmonizing a G major scale can be put together to establish a chord progression for a song. A lead guitar player could play along with that for his solo. He should've taught you about functional chord progressions and discussed tonic, predominant and dominant chords. If he tried to talk about modes without teaching you functional harmony, I suggest you fire this man immediately.
Nothing that is worthwhile in life will ever come easy.
No he didn't my previous teacher did, this teacher is new for me. My previous teacher just taught me basic modes, and penatonics. Previously I didn't know many notes at all on the strings but the new teacher taught me them and several other things first lesson, after that I said that was pretty easy so he stepped it up A LOT and went really in depth. He told me about 12-TET Intervals, and about stacking intervals. I am completely confused to what the numbers in the TET even relate to is what the major problem is. I really need a good website to help me out with this.
I would start with telling your teacher that you didn't understand what he was saying, and that he should reexplain it, or tone it down a bit.

A good website for music theory is musictheory.net
Thanks, and yea I am going to tell him that for sure but I dont want to make that whole lesson a waste so I'm just going to study it.
Quote by ToneMasterDelux
Thanks, and yea I am going to tell him that for sure but I dont want to make that whole lesson a waste so I'm just going to study it.

Sure thing. To get the most out of the lessons always talk back to the teacher, to let them know what you understand or don't understand. Just saying something is "pretty easy" isn't enough, re-iterate things that are taught and tell him to slow down if you get completely lost. Even if it gets to the point where you only learn one thing in a lesson, it's still better than nothing.
And no, Guitar Hero will not help. Even on expert. Really.