I know how you feel actually. As I said in my previous post I spent half of the time I have been playing, almost 20 years now, not really knowing any theory other than the shapes and so on that I had familiarised myself with. I couldn't have even told you what the major scale is until I had already been playing for ten years or more and by then I had even done a fair amount of gigging and recording. I basically wrote anything I wrote based on the way certain shapes 'sounded' or I would hum something and try to play it. Usually I found that I had a certain idea in my head and I could never really figure out how to realise it musically.
I am actually pretty much self-taught in my knowledge of music theory. I have done a lot of reading and I have worked in situations with more formally trained musicians and spent a lot of time discussing different ideas with them. I also developed my theoretical knowledge by writing and analysing what I was doing and also by analysing what other people do. This is also an ongoing process. The language of music theory can get pretty confusing, though and one problem I found that limited me early on was that a lot of the ideas that are involved in music theory are rarely ever explained in an empirical sense. Usually people will teach a scale or a mode and just say "play this in A", for example and not really explain how scales, triads, intervals, chords etc are linked.
I would recommend getting a good tutor, and not someone who is just going to teach you licks and so on. You really want to be specific too when you ask a tutor about tuition, and tell them that you want to learn what certain things mean, not just how to play them. In my opinion if you go to a tutor and the first thing they tell you isn't that the major scale is formed by playing all the natural notes from C-C on a piano and then explaining how you derive the intervals and consequently the basic units of comparison and 'measurement' for all scales, intevals, chords etc, then don't waste your time and money with them. Sometimes I think getting someone to teach you at least those basic concepts can make a lot of difference in your overal development of theory.
The internet is full of good resources for learning about theory too.
http://www.dolmetsch.comis one that I would recommend as it starts right from the very basics and goes into very advanced concepts.
I think you are right in saying it is never too late to learn though. I think also that the toughest thing is to break old habits and attitudes. I remember very clearly my attitude to theory before I really got involved in learning about it and understanding it, and the difference between what I was able to do then and what I am able to do now. I know now that all my claims of being able to play it by ear were less than accurate for the most part, and the way I see it now, it doesn't matter how well I can hear something, what is the point if my mind can't interpret it in a relative sense for me to play?
Anyway good luck. If you have any specific questions you want to ask me feel free to send me a message. I don't mind reading stuff and replying in the forum as long as Mr Hippy is cool about it too.