Well.... for the immediate use I suggest using vinegar. White vinegar, like you get at the grocery store, will cut a lot of the buildup you have... that white/yellowish stuff on the wood. My rabbits don't mind the vinegar smell and that doesn't last long at all. Poor it over the wood, let it sit for a few minutes and then scrub it with a brush, rinse and splash more vinegar on it. You don't need to rinse off the last splash of vinegar. I use the vinegar full strength.
Spalding Labs has a product that I use in my rabbitry that kills odors. I use this with the rabbits and goats. It really works well.
Bye Bye Odor is what it is called. It is a concentrate you mix with water and then spray. I've used it with new chicks in the house with great success.
www.spalding-labs.com/products/odor_control_products/default.aspx
Unfortunately your choice of wood may make this odor problem ongoing... I won't fault you for using wood, as one must work within one's budget and you want the best for your animals based on what you can afford/do. So some ideas on how to keep the urine from soaking into the wood would be using a sealant on any wood that the rabbits could not gnaw on. Maybe a gloss enamel in a light color would work well for you. Get as much of the build up off the walls as you can, dry out the hutch, and put down a couple coats of enamel or paint... something scrub-able. That way next time you do a deep clean the buildup, which will still happen, will come off much easier since the urine can't get to the wood.
Your set-up looks good, you are providing your rabbits with air, shade and it looks like you tack up plastic to keep the winter off of them. Bravo for using their droppings in the garden. The odor problem can be fixed but it will take some work to do so. There isn't a magic potion. Believe me, I've searched for one for a long, long time.
What kind of rabbits are you raising? I have Cali/NZ crosses for meat.
Please keep us posted on your progress, welcome to BYH. We are glad you found us and ticked pink to have you contribute to our combined knowledge. There are a bunch of rabbit folk here. Oh, and we love pictures... please and thank you.