Thanks everyone for your input.
I have my mount apart inside and I've found a few things. I probably did have the gearbox mounted off-axis when I replaced it the other day.? Inside, comparing the new gearbox with the old one, I can see that the mounting holes on the gearbox, where it goes over the threaded rods coming out of the mount, the holes on the new gearbox are smaller, which explains why I had so much trouble getting it on.? The old gearbox came with the holes slightly enlarged!
I'm enlarged the holes on my new gearbox now, and once I finish the cleaning and regreasing, I'll see how it works once reassembled.
I know about the adjustment on the Ovision worms and I will check that more, but I'm slightly concerned with how rough the RA worm feels now that I have it out, compared to the Dec worm. I'll check whether that is a lubrication issue or a tension issue with the adjustment screw.
Thanks again for all the advice.
-Joe