Slow practice, over and over again, of everything from scales to hymns to Bach pedal solos. The slower the practice tempo, the faster you will be able to play accurately.

Second to everything said above. I practice dirt slow and exaggerate every motion, which is a technique I learned when studying drum rudiments. It works on wind instruments, too. After I feel comfortable with the motions, and I feel like I've got the notes and rhythms down, I speed up gradually. Pedal scales are probably the most useful tools.

Organ shoes can be expensive, but they're totally worth it. If money is an issue, as it is for me, this is what you can do, and is what I did to improvise: you can go to Goodwill or other type of store and buy a pair of used dress shoes a half size smaller than you usually wear. I did this on purpose in order to make sure they'd be thin enough. You also have to make sure that you take a look at the construction of the shoe, and make sure that there isn't some odd protrusion that will hit other notes when you're not expecting it. That's why I specify a dress shoe, because they are generally of straightforward construction.

I have found contrary motion with pedal/manual scales to be helpful. Slowly, of course.

with advice on some of the posts above, another important thing is to keep knees and feet together

knees together is not a mechanical rule, it's an attitude of posture depending upon each individual. if you adopt the right attitude towards this technique it will definitely help accuracy

my legs, knees and feet do not stay together, but the attitude to do so has improved accuracy

I sometimes find it difficult to keep knees and feet together when playing notes at the extreme ends of the pedalboard, so I usually don't. At the extremes, I usually just try to keep knees together, but I often forget. When playing more in the center, I try to keep feet together at least. That seems to help accuracy and the sense of preparedness to play using the pedals.

Antonio:

Yes, changing between organs with different scaling can cause issues. I play the Roland C330 here and there for gigs, and the European pedalboard is a tad wider and can cause issues with wide intervals as the distance becomes exponentially greater and sometimes results in the frustrating double note under reach.

I use exercises out of tutor methods to get back up to scratch. There is a green and white stripey book that's good but I cannot remember the name of it. It's something like the complete guide to the organ.
Also, practicing pedal separate to the hymn is good and then practising left hand and pedal is good. I know it's a bit of a no no but play the pedal note in your left hand as well as the pedal when you do that, it does improve things.
I also like to sing all the parts (one at a time) whilst doing this, it helps me to "breathe" with the music too.

Not yet mentioned: your position on the bench, your feet position on the pedalboard, and bench height. You should sit centered on the console, i.e. with middle F# on the keyboard (61 notes, more like middle D# on 56 notes). You should be able to move your thighs and knees up and down, so don't sit too far back. Your foot should rest, naturally, above the middle notes of the pedalboard, on but not depressing the naturals, toes just barely touching the sharps. I used to carry 2x4 cut-offs with me to raise benches where i visited. (I left them in a practice room at Northwestern University, and they were still floating around from room to room 10 years later!) Just as your fingers should be able to feel the gaps between the sharps as you play on the manuals, your feet can feel the gaps on the pedals.