So much of that sounds familiar! I'm sure many people have struggled with the same feelings - I certainly did for a long time. There's much I could say in response, but I'll try and keep it reasonably brief. These are just personal comments, of course - others may disagree!
In the end, I think the point of learning music is to perform it for other people. I really think that's the bottom line. I've found that without that motivation, it becomes hard to sustain the effort to polish a piece. Of course, finding appropriate performance opportunities on the organ isn't easy. If you have a good teacher, they should be able to help, or try making friends with a local organist, and offering to play the occasional voluntary, or short piece before the service. Every occasion where you get put on the spot and have to play something for an 'audience' is helpful - so long as you're prepared and focused, and so long as the 'audience' is supportive.
In connection with that - be patient. Even when you've nearly learned all the notes, there's a lot of work needed to polish a confident and fluent performance of a major work - but when you do, it's a joyful experience to play for others. Taking the opportunity to play for others in informal settings while learning a piece is very useful - e.g. for a teacher, or for another organist friend. Approach it like a performance and do your best. Then evaluate, adjust and do some more practice.
Very important - learn to practice efficiently. You can do a lot of good in a short time if you focus on problem corners and work at them. Practice in short bursts - notice when you get tired and take a break. Do hands and feet separately, repeat short sections and take everything as slowly as necessary to get the right notes, right fingerings and right articulation. It may feel plodding, but it will help. A friend recently told me to 'practice with no expectation of improvement' - sounds counter-intuitive, but it works. Sometimes, it just takes time for the subconscious to process and assimilate a piece.
Take time to work on the fundamentals - posture, relaxed muscles, hand position, neat, easeful movement, articulation, mental focus.
Learn a mix of music - work on the big stuff (and be prepared for how long it will take), but also tackle music well within your capabilities - pieces you can learn and perform in a few weeks - this will boost your confidence and motivation. There are lots of medium-difficulty anthologies around. Also - learn some manuals-only repertoire (e.g. Sweelinck, Byrd, English 18th C music, or 19th C harmonium repertoire) - great for articulation.
Sorry - this has turned into advice on practising. I guess my experience is that if one learns to practice well, and has appropriate, manageable performance opportunities, motivation isn't a problem. A couple of years ago, I felt very much like you do, but these days, I practice almost every day - even if only for 15 minutes.
Last thing - I found this book very useful indeed:http://ukcatalogue.oup.com/product/9780 ... lKIGKzfF-g
Have fun, and don't get discouraged! I honestly don't think you've reached the limit of what you can achieve.