I started on organ, it was a small church just with organ and drums, and young musicians were taught you should be able to play everything with your weak hand, that you could with your dominant, and that the pedals were there for use...so even as a primary player I could use pedals. Now at our local church, I primarily play piano(piano patches anyway)...so for the past two years when doing services for others ,concerts, or in the studio is the only time I actually play organ. So because I dont play organ regularly anymore, I have to schedule time to practice, just to keep my self fluent, and I notice that the bulk of the stumble comes from pedals....now mind you, up until 2 years ago I was an organist, so I've always been strong in pedals...even in fast rejoicing music, I would not left hand the bass, but I guess like other things, when you don't continue at it.....
Like most of you ,my chord structure and phrasing is different on organ than piano...so I spend dedicated time practicing both. I'm fluent in all keys, but I've gained fluency in D,G, and A just in the past years that I've been primarily on piano.....So I have to still practice those keys on organ, my chording and handwork is fine,but my feet don't automatically go to the correct pedal (without thinking)...and I HATE having to look at the pedals when I play(reminds me of my starting days, could never watch the choir director, because I had to watch and make sure my hands and feet were in proper position)
The other hinderance is that I'm 6'8, which was great for playing ball, but not so good for running pedals comfortably.